Re: [gmx-users] Heat of vap

On 2011-04-03 02.15, Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: *one singl

Re: [gmx-users] Simulation Crash...Reg

Kishore wrote: Dear All, I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in simple spc water in a dodecahedron box. I could easily walk through till the NVT equilibration step after which every thing seems so right(after 5 steps with time step of 2fs using V-rescale t

[gmx-users] domain decomposition

Dear All I have a file which contains afew residues (noncontinuous), When I use mdrun on a computer(4 cpu) I am facing with the following Error: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 3.28697 nm Change the number

Re: [gmx-users] domain decomposition

On 4/04/2011 1:51 AM, mohsen ramezanpour wrote: Dear All I have a file which contains afew residues (noncontinuous), When I use mdrun on a computer(4 cpu) I am facing with the following Error: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and

[gmx-users] gromacs 4.5.4 analysis tools

Dear gmx users, I’m a NAMD user and want to use gromacs 4.5.4 analysis tools for my NAMD output files. I have some NAMD output files : output.coor , output.vel , output.dcd (binary coordinate trajectory output file). Can I convert these output files into gromacs output files and use gromacs 4.5.

Re: [gmx-users] gromacs 4.5.4 analysis tools

Hi, depends on the tool. If the tool just need the coordinates or just velocities (dcd/vel) you don't need to convert anything because the tools can use the VMD plugins to read dcd. If the tool needs a tpr file (e.g. carges) than you need to create one. In most cases the easiest solution to do thi

Re: [gmx-users] Heat of vap

> > Elisabeth wrote: > >> Dear David, >> >> I followed your instructions and calculated Heat of vaporization of my >> alkane once with one molecule in gas phase (no cutoff) and once with >> equivalent number of molecules as in liquid phase as Justin suggested. >> Results are as follows: >> >> > To

Re: [gmx-users] Heat of vap

Elisabeth wrote: Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin

[gmx-users] Re:Simulation Crash

Dear Justin, I have used the same .mdp file you have used in your tutorial for enzyme-ligand complex, I am pasting it here. My system consists of 10212 (enzyme+NADPH) atoms and 45000 water molecules. title = Protein-ligand complex NPT equilibration define = -DPOSRES ; position restrain

Re: [gmx-users] Re:Simulation Crash

Kishore wrote: Dear Justin, I have used the same .mdp file you have used in your tutorial for enzyme-ligand complex, I am pasting it here. My system consists of 10212 (enzyme+NADPH) atoms and 45000 water molecules. Try using the Berendsen barostat instead of P-R. Some systems don't behav

[gmx-users] Defined number of molecule of water into box

Dear all, is it possible to put into a box a defined number of particle?in other word, i'd like put into my system eg. 100 molecule of water, I tried with: genbox -cp protein.gro -cs -nmol 100 -try 1 -o out.gro but it does not work.Can you help me? Thanks! Anna -- gmx-users mailing listgmx

Re: [gmx-users] Heat of vap

On 2011-04-04 01.32, Justin A. Lemkul wrote: Elisabeth wrote: Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Just