[gmx-users] call for help

Hello, gmx-users, I have some problems with the gmxdump order. How to transform the traj.trr to another readable file every two steps? In another word, there are 1 frames in the traj.trr file. I would like to transform datas every second frame in the traj.trr to another readable file.

Re: [gmx-users] Bad .tpr or .xtc files?

Hi Peggy, This is very much basic stuff for which you should refer to the manual/wiki. E.g. on the index file, look at http://wiki.gromacs.org/index.php/Index_File For the other questions, check the manpages of editconf, trjconv and tpbconv. Cheers, Tsjerk On Thu, Apr 10, 2008 at 11:03 PM,

Re: [gmx-users] call for help

曹臻 wrote: Hello, gmx-users, I have some problems with the gmxdump order. How to transform the traj.trr to another readable file every two steps? In another word, there are 1 frames in the traj.trr file. I would like to transform datas every second frame in the traj.trr to another

Re: [gmx-users] Wrong heat capacity (water)

Andreas Kring wrote: Hello all, I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This works out fine, i.e. I get a correct radial distribution function (g_OO), but the heat capacity (C_V) is wrong. I

[gmx-users] Wrong heat capacity (water)

Hello all, I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This works out fine, i.e. I get a correct radial distribution function (g_OO), but the heat capacity (C_V) is wrong. I calculated it using the

[gmx-users] mpi error

Dear all, I had been running many runs of mdrun in a Sun opteron cluster with each node having 4 processors. When I ran my latest mdrun after 15ns run, I get the following error and mdrun exits without any error message on other log files. ***

[gmx-users] Epsilon in ffoplsaanb.itp

Dear list, The OPLS parameter for S in DMSO is zigma 0.395 and epsilon 3.56 A ( JACS 1996, 118, 4175-4180) But in the ffoplsaanb.itp (/gromacs/3.3.2-dp/share/gromacs/top) it is given as below: - name bond_typemass

Re: [gmx-users] mpi error

Ragothaman Yennamalli wrote: Dear all, I had been running many runs of mdrun in a Sun opteron cluster with each node having 4 processors. When I ran my latest mdrun after 15ns run, I get the following error and mdrun exits without any error message on other log files.

[gmx-users] call for help about the hydration number

Hi all How can I count the number of water molecules within spheres of desired radii around a solute when I analyse the trajectory.Thank you in advance! ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] call for help about the hydration number

[EMAIL PROTECTED] skrev: Hi all How can I count the number of water molecules within spheres of desired radii around a solute when I analyse the trajectory.Thank you in advance! ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Epsilon in ffoplsaanb.itp

JMandumpal wrote: Dear list, The OPLS parameter for S in DMSO is zigma 0.395 and epsilon 3.56 A ( JACS 1996, 118, 4175-4180) But in the ffoplsaanb.itp (/gromacs/3.3.2-dp/share/gromacs/top) it is given as below: - name

[gmx-users] dynamic of a peptide in a mixture TFE/H2O ( 30/70 %)

I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %). I'm using this file.mdp : cpp = /lib/cpp define = -DFLEX_SPC -DPOSRES constraints = all-bonds integrator = md tinit = 0.0 dt = 0.002 ; ps ! nsteps = 50 ; total 1000 ps. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0

Re: [gmx-users] Bad .tpr or .xtc files?

Thank you, Tsjerk. I will check them out. But I am still confursed with what has gone wrong. As I said in my previous eamil, in fact, 2 Ca atoms are a part of the protein. They are in the PDB file passed to pdb2gmx. Water molecules are added after the protein atoms and the Ca atoms, as in the PDB

[gmx-users] CO2.pdb

Dear gmx-users, Greetings. I try to have methane pdb. or CO2.pdb to understand basically how to have a vibrational mode. But I have problem with imput pbd file. ATOM 1 C1METH1 3.875 0.678 -8.417 1.00 0.00 ATOM 2 H1 METH1 3.800 1.690 -8.076 1.00

[gmx-users] Co2.pdb

Hello, Your atoms coordinates are too far away from each other. Try to paste the text below into a new text file. Make sure to rename it to a .pdb extension. Voila! Cheers. Ps. This is a Methan molecule. HEADER METHANE HETATM1 C 1 0.257

[gmx-users] MTH force field

Dear all. Please, How can I do to have MTH this force field. MTH ffgmx.rtp - methanolCH3OH Thanks a lot ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] MTH force field

Collins Nganou wrote: Dear all. Please, How can I do to have MTH this force field. MTH ffgmx.rtp - methanolCH3OH Firstly, you haven't described what you are trying to do. Secondly, ffgmx is deprecated, and should not be used for new simulations. Mark

[gmx-users] a problem about the residence

Thank you for your reply, integrate the rdf can only provide the average hydration number, but I want to calcualte the dependence of hydration on the time, namely the number of water molecules within the some radii around the solute. In your mail: From: David van der Spoel [EMAIL PROTECTED]

Re: [gmx-users] a problem about the residence

You can actually do what you want in VMD. Cheers, Michel On Fri, Apr 11, 2008 at 10:38 PM, [EMAIL PROTECTED] wrote: Thank you for your reply, integrate the rdf can only provide the average hydration number, but I want to calcualte the dependence of hydration on the time, namely the

Re: [gmx-users] a problem about the residence

[EMAIL PROTECTED] wrote: Thank you for your reply, integrate the rdf can only provide the average hydration number, but I want to calcualte the dependence of hydration on the time, namely the number of water molecules within the some radii around the solute. So partition your trajectory