Re: [gmx-users] segmentation fault

2011-01-15 Thread leila separdar
I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about

Re: [gmx-users] CNT

2011-01-15 Thread Justin A. Lemkul
trevor brown wrote: Dear users, In Gromacs 4.5.3, atom types are defined in /share/top/oplsaa.ff/atomtypes.atp. The corresponding bonds for diffrent atopm pairs are described as between opls_001 and opls_965. I have a CNT, I need C-C intereaction, which one should I choose? I would find a

[gmx-users] CNT

2011-01-15 Thread trevor brown
Dear users, In Gromacs 4.5.3, atom types are defined in /share/top/oplsaa.ff/atomtypes.atp. The corresponding bonds for diffrent atopm pairs are described as between opls_001 and opls_965. I have a CNT, I need C-C intereaction, which one should I choose? Second question; where can I find info about

Re: [gmx-users] segmentation fault

2011-01-15 Thread Mark Abraham
On 15/01/2011 8:50 PM, leila separdar wrote: I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tp

Re: [gmx-users] g_covar

2011-01-15 Thread Tsjerk Wassenaar
Hi Karbalee, It says : nanometer squared. Cheers, Tsjerk PS. Many of us are not Justin... :p On Sat, Jan 15, 2011 at 5:33 PM, shahrbanoo karbalaee wrote: > Dear Justin > Hi,I want to use PCA for compare fluctuations two  peptides with  13 > aa. I  use this command g_covar > g_covar #NAME?  ru

[gmx-users] g_covar

2011-01-15 Thread shahrbanoo karbalaee
Dear Justin Hi,I want to use PCA for compare fluctuations two peptides with 13 aa. I use this command g_covar g_covar #NAME? run2.tpr#NAME? run2.xtc#NAME? eigenvaluesbackbone.xvg #NAME? eigenvectorsbackbone.trr#NAME? covarbackbon.xpm and get the some of data : ti

Re: [gmx-users] so difficult problem

2011-01-15 Thread Justin A. Lemkul
mohsen ramezanpour wrote: I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make fo

Re: [gmx-users] so difficult problem

2011-01-15 Thread mohsen ramezanpour
I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make force less. please let me know how

[gmx-users] segmentation fault

2011-01-15 Thread leila separdar
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tpr, VERSION 4.0.7 (single precision) Back Off! I