[gmx-users] about command do_dssp

Dear prof. i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use the do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg to analyze the secondary structrue of the protein. when i perform the do_dssp and select MainChain , the fatal

Re: [gmx-users] Including polarizability by a Drude oscillator or the shell model

On 2013-04-27 19:18, Andrew DeYoung wrote: Hi, I am interested in including polarizability using a Drude harmonic oscillator (charge on a spring). In section 3.5 of the version 4.5.4 manual, Shell molecular dynamics is described briefly. It seems that the shell model is quite similar, if not

[gmx-users] can we use large timestep for membrane GPU simulation?

Hello: I am watching Eric online Gromacs GPU webminar these days. I notice that he talked about introduce large timestep (5fs) for GPU simulations on a water system. I am just wondering, can we also introduce such big time step for membrane system if we are going to run the job in Gromacs?

Re: [gmx-users] about command do_dssp

On 4/28/13 4:07 AM, aixintiankong wrote: Dear prof. i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use the do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg to analyze the secondary structrue of the protein. when i perform

[gmx-users] why files are so large?

Hello: I am using the following settings for output file: dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout = 500 ; Write coordinates to

Re: [gmx-users] can we use large timestep for membrane GPU simulation?

On 4/28/13 6:15 AM, Albert wrote: Hello: I am watching Eric online Gromacs GPU webminar these days. I notice that he talked about introduce large timestep (5fs) for GPU simulations on a water system. I am just wondering, can we also introduce such big time step for membrane system if we

Re: [gmx-users] why files are so large?

On 4/28/13 8:04 AM, Albert wrote: Hello: I am using the following settings for output file: dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout = 500

Re: [gmx-users] why files are so large?

On 04/28/2013 02:08 PM, Justin Lemkul wrote: This looks like a pretty clear bug to me, especially the negative file size, which cannot possibly make sense. What version of Gromacs is this? -Justin hi Justin: thanks a lot for kind comments. I am using the latest 4.6.1 with GPU production.

Re: [gmx-users] why files are so large?

On 4/28/13 8:09 AM, Albert wrote: On 04/28/2013 02:08 PM, Justin Lemkul wrote: This looks like a pretty clear bug to me, especially the negative file size, which cannot possibly make sense. What version of Gromacs is this? -Justin hi Justin: thanks a lot for kind comments. I am using

[gmx-users] GPU job often stopped

Dear: I am running MD jobs in a workstation with 4 K20 GPU and I found that the job always failed with following messages from time to time: [tesla:03432] *** Process received signal *** [tesla:03432] Signal: Segmentation fault (11) [tesla:03432] Signal code: Address not mapped (1)

Re: [gmx-users] GPU job often stopped

On 4/28/13 11:27 AM, Albert wrote: Dear: I am running MD jobs in a workstation with 4 K20 GPU and I found that the job always failed with following messages from time to time: [tesla:03432] *** Process received signal *** [tesla:03432] Signal: Segmentation fault (11) [tesla:03432] Signal