This is a common issue when you use chimera for minimization and MD. all you need is to wait for results "Not responding "doesn't mean it doesn't run". Since you are not from CS background ,Get used to NAMD alongwith VMD. This has got quickMD extension for Novices which might help you.
This is a common issue when you use chimera for minimization and MD. all you need is to wait for results "Not responding "doesn't mean it doesn't run". Since you are not from CS background ,Get used to NAMD alongwith VMD. This has got quickMD extension for Novices which might help you.
I think it's not a good practice to simulate a system using UCSF chimera. Time has changed.... I would suggest you to use GROMACS (free, and a good one) or if you can pay for AMBER, CHARM, DESMOND etc. And as far as I know, you can easily find and solve any error in GROMACS and same is the case with AMBER etc. There're some good newbie GROMACS tutorials too. Follow Justin Lemkul tutorial.
I think it's not a good practice to simulate a system using UCSF chimera. Time has changed.... I would suggest you to use GROMACS (free, and a good one) or if you can pay for AMBER, CHARM, DESMOND etc. And as far as I know, you can easily find and solve any error in GROMACS and same is the case with AMBER etc. There're some good newbie GROMACS tutorials too. Follow Justin Lemkul tutorial.
Dear Sir, In this case, you can reduce the number of runs because MD in chimera uses lot of memory and RAM. It took a lot of time (8 hours) in intel i-3 processor 4 GB RAM for 1000 runs, meanwhile, it shows not responding. Be patient and you will get the result. I also used i-5 processor (8 GB RAM). Either you can reduce the number of runs to 100 or so to get the work done faster.
Dear Sir, In this case, you can reduce the number of runs because MD in chimera uses lot of memory and RAM. It took a lot of time (8 hours) in intel i-3 processor 4 GB RAM for 1000 runs, meanwhile, it shows not responding. Be patient and you will get the result. I also used i-5 processor (8 GB RAM). Either you can reduce the number of runs to 100 or so to get the work done faster.
SAMEE ULLAH Thanks for your response. The problem is I am not from CS background and GROMACS does not run in Windows OS (easily). Even I have tried to install it in Ubuntu but failed. :)
SAMEE ULLAH Thanks for your response. The problem is I am not from CS background and GROMACS does not run in Windows OS (easily). Even I have tried to install it in Ubuntu but failed. :)
It's not advisable to run MD on chimera interface. Chimera is just good visualizer and can work with plugins like modeller, autodock etc. Just install Gromacs on windows as per earlier suggestions (@samee ullah) or compile it through cygwin. Another easy way in windows is to install virtual box and ubuntu OS. I havn't found any other easier way than to use Gromacs or other MD programs through linux or cygwin commands. Regards
It's not advisable to run MD on chimera interface. Chimera is just good visualizer and can work with plugins like modeller, autodock etc. Just install Gromacs on windows as per earlier suggestions (@samee ullah) or compile it through cygwin. Another easy way in windows is to install virtual box and ubuntu OS. I havn't found any other easier way than to use Gromacs or other MD programs through linux or cygwin commands. Regards
Hello, everyone..I got the same issue as I begun a MD it finished and then got to "Not responding mode", but I understand and still waiting for it to finish. I got VMD/Namd2 for MD, yet I do really enjoy the graphics and analysis interface of Chimera. Question is Can I run MD in VMD/Namd2 and do analysis on Chimera? How can I import MD data from VMD into Chimera? Thanks.
Hello, everyone..I got the same issue as I begun a MD it finished and then got to "Not responding mode", but I understand and still waiting for it to finish. I got VMD/Namd2 for MD, yet I do really enjoy the graphics and analysis interface of Chimera. Question is Can I run MD in VMD/Namd2 and do analysis on Chimera? How can I import MD data from VMD into Chimera? Thanks.
Wait means sometime for days, programs are designed not to respond while performing lengthy calculations, Once the calculation is done it will start responding again.
Wait means sometime for days, programs are designed not to respond while performing lengthy calculations, Once the calculation is done it will start responding again.
Venkataraghavan Can you please let me know the detail how to run MD simulations of protein-ligand complex using Chimera.
Venkataraghavan Can you please let me know the detail how to run MD simulations of protein-ligand complex using Chimera.
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Ranabir Majumder There are good tutorials on how to install GROMACS in windows as well as linux.
Please use these one;
https://www.youtube.com/watch?v=S6n5dRVMM7w
https://www.youtube.com/watch?v=x3ypo2Oegvc
Ranabir Majumder There are good tutorials on how to install GROMACS in windows as well as linux.
Please use these one;
https://www.youtube.com/watch?v=S6n5dRVMM7w
https://www.youtube.com/watch?v=x3ypo2Oegvc
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VOTE
This is a common issue when you use chimera for minimization and MD. all you need is to wait for results "Not responding "doesn't mean it doesn't run". Since you are not from CS background ,Get used to NAMD alongwith VMD. This has got quickMD extension for Novices which might help you.
This is a common issue when you use chimera for minimization and MD. all you need is to wait for results "Not responding "doesn't mean it doesn't run". Since you are not from CS background ,Get used to NAMD alongwith VMD. This has got quickMD extension for Novices which might help you.
More
VOTE
Chimera usually used for the visualization purpose. you may have to try gromacs or namd
Chimera usually used for the visualization purpose. you may have to try gromacs or namd
More
VOTE
I think it's not a good practice to simulate a system using UCSF chimera.
Time has changed....
I would suggest you to use GROMACS (free, and a good one) or if you can pay for AMBER, CHARM, DESMOND etc.
And as far as I know, you can easily find and solve any error in GROMACS and same is the case with AMBER etc. There're some good newbie GROMACS tutorials too. Follow Justin Lemkul tutorial.
You just need a new tool only.
I think it's not a good practice to simulate a system using UCSF chimera.
Time has changed....
I would suggest you to use GROMACS (free, and a good one) or if you can pay for AMBER, CHARM, DESMOND etc.
And as far as I know, you can easily find and solve any error in GROMACS and same is the case with AMBER etc. There're some good newbie GROMACS tutorials too. Follow Justin Lemkul tutorial.
You just need a new tool only.
More
VOTE
Dear Sir, In this case, you can reduce the number of runs because MD in chimera uses lot of memory and RAM. It took a lot of time (8 hours) in intel i-3 processor 4 GB RAM for 1000 runs, meanwhile, it shows not responding. Be patient and you will get the result. I also used i-5 processor (8 GB RAM). Either you can reduce the number of runs to 100 or so to get the work done faster.
Dear Sir, In this case, you can reduce the number of runs because MD in chimera uses lot of memory and RAM. It took a lot of time (8 hours) in intel i-3 processor 4 GB RAM for 1000 runs, meanwhile, it shows not responding. Be patient and you will get the result. I also used i-5 processor (8 GB RAM). Either you can reduce the number of runs to 100 or so to get the work done faster.
More
VOTE
SAMEE ULLAH Thanks for your response. The problem is I am not from CS background and GROMACS does not run in Windows OS (easily). Even I have tried to install it in Ubuntu but failed. :)
SAMEE ULLAH Thanks for your response. The problem is I am not from CS background and GROMACS does not run in Windows OS (easily). Even I have tried to install it in Ubuntu but failed. :)
More
VOTE
It's not advisable to run MD on chimera interface. Chimera is just good visualizer and can work with plugins like modeller, autodock etc. Just install Gromacs on windows as per earlier suggestions (@samee ullah) or compile it through cygwin. Another easy way in windows is to install virtual box and ubuntu OS. I havn't found any other easier way than to use Gromacs or other MD programs through linux or cygwin commands.
Regards
It's not advisable to run MD on chimera interface. Chimera is just good visualizer and can work with plugins like modeller, autodock etc. Just install Gromacs on windows as per earlier suggestions (@samee ullah) or compile it through cygwin. Another easy way in windows is to install virtual box and ubuntu OS. I havn't found any other easier way than to use Gromacs or other MD programs through linux or cygwin commands.
Regards
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Hello, everyone..I got the same issue as I begun a MD it finished and then got to "Not responding mode", but I understand and still waiting for it to finish. I got VMD/Namd2 for MD, yet I do really enjoy the graphics and analysis interface of Chimera. Question is Can I run MD in VMD/Namd2 and do analysis on Chimera? How can I import MD data from VMD into Chimera? Thanks.
Hello, everyone..I got the same issue as I begun a MD it finished and then got to "Not responding mode", but I understand and still waiting for it to finish. I got VMD/Namd2 for MD, yet I do really enjoy the graphics and analysis interface of Chimera. Question is Can I run MD in VMD/Namd2 and do analysis on Chimera? How can I import MD data from VMD into Chimera? Thanks.
More
VOTE
Wait means sometime for days, programs are designed not to respond while performing lengthy calculations, Once the calculation is done it will start responding again.
Wait means sometime for days, programs are designed not to respond while performing lengthy calculations, Once the calculation is done it will start responding again.
More
VOTE