Re: [gmx-users] trajectory output from g_select ?

Ok, I'll try the python solution Thanks for your help, Jonathan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe

[gmx-users] Vectors in non-cubic box

Hi, I want to create *.gro file with simulation box size as following: 3.460467452 0. 0. 1.730233726 2.9968527222000 0. 0. 0. 10.00 I used the command: ]editconf –f *.pdb –o *.

Re: [gmx-users] Vectors in non-cubic box

Hi Afsaneh, The PBC and the .gro file format are explained in the manual, chapter 3. The last line of the .gro file has the box stored as XX YY ZZ XY XZ YX YZ ZX ZY Cheers, Tsjerk On Mar 5, 2011 6:03 AM, "afsaneh maleki" wrote: Hi, I want to create *.gro file with simulation box size as fo

Re: [gmx-users] Vectors in non-cubic box

Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searc

Re: [gmx-users] Vectors in non-cubic box

Hi Afsaneh, Sorry for missing out on that one. Yes, all tools properly deal with tric. cells. Cheers, Tsjerk On Mar 5, 2011 7:24 AM, "afsaneh maleki" wrote: Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- gmx-users mailing li

Re: [gmx-users] mdrun-gpu

Dear Natalia, The current mdrun-gpu (which btw uses OpenMM) is capable to run a single simulation, on a single node, using a single GPU only. Cheers, -- Szilárd On Fri, Mar 4, 2011 at 6:28 PM, Nathalia Garces wrote: > Hello, > I want to know if it is possible to use "mdrun-gpu" with the comma

[gmx-users] Warning: 1-4 interaction

Hi everyone, My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything works fine till the

Re: [gmx-users] Warning: 1-4 interaction

Moeed wrote: Hi everyone, My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything

Re: [gmx-users] Warning: 1-4 interaction

On 06/03/11, Moeed wrote: > Hi everyone, > > My attempt to conduct a NPT failed although everything seemed to be going > well. Topology is OK and I am just curious why system is blowing up all of a > sudden towards the end of simulation. I should mention that by changing > fourierspacing fr

Re: [gmx-users] Warning: 1-4 interaction

Hello Justin, I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance between fourierspacing a

Re: [gmx-users] Warning: 1-4 interaction

Moeed wrote: Hello Justin, I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance betw