[gmx-users] Questions about CO2.

Dear all, I went through the mails about the use of virtual sites for representing linear molecules like CO2. I also read that GROMACS cannot handle angle bending potentials at 180 degrees in an appropriate manner. My system consists of EPM2-CO2 dissollved in TIP4- H2O. I ma

[gmx-users] length of beta sheet

Hi everyone, I would like to calculate length of beta sheet. Is this any automatic tool to serve the purpose? To elaborate, I am aware that dssp can give me whether the residue is in beta sheet ("E") or not at each time frame but I want to know exactly how many hydrogen bonds are formed by each re

[gmx-users] Pulling code

Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define i

Re: [gmx-users] initial velocities

Many thanks Tsjerk and Justin! You both helped alot. Regards, Mah On Wed, Dec 24, 2014 at 10:10 PM, mah maz wrote: > Thank you very much Tsjerk! As far as I know .gro files are coordinate > ones, containing the structure of the system. How is it possible to make > difference between x,y and z A

Re: [gmx-users] Error in topology using g_x2top

On 12/24/14 1:39 AM, Rajan Kumar wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of Hydroxyl and epoxide group on only one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the sam

Re: [gmx-users] initial velocities

On 12/24/14 2:17 PM, Tsjerk Wassenaar wrote: Hi Mah, You can add velocities after the coordinates, in the same format, usually %8.3f %8.4f for velocities, coordinates are %8.3f :) http://manual.gromacs.org/online/gro.html -Justin -- == Jus

Re: [gmx-users] initial velocities

Hi Mah, You can add velocities after the coordinates, in the same format, usually %8.3f Cheers, Tsjerk On Dec 24, 2014 7:41 PM, "mah maz" wrote: > Thank you very much Tsjerk! As far as I know .gro files are coordinate > ones, containing the structure of the system. How is it possible to make >

Re: [gmx-users] initial velocities

Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference between x,y and z AND vx,vy and vz? Should I write the file like coordinate format? Regards, Mah On Wed, Dec 24, 2014 at 7:44 PM, mah maz wrot

Re: [gmx-users] initial velocities

Hi Mah Maz, The easiest way is to write a .gro file with the velocities you want and use that as input. Cheers, Tsjerk On Dec 24, 2014 5:14 PM, "mah maz" wrote: > Dear all, > > I want to apply an initial velocity to my system. Is there a possible > way rather than gen_vel in which I can chose

[gmx-users] initial velocities

Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://ww

Re: [gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)

On 2014-12-24 15:33, Amit Kumawat wrote: Dear Gromacs Users, I have a trajectory of 2microsecond. I am trying to use gmxcheck to analyse trajectory but I am getting following error; Program gmxcheck, VERSION 4.6.5 Source code file: /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c, line: 92

[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)

Dear Gromacs Users, I have a trajectory of 2microsecond. I am trying to use gmxcheck to analyse trajectory but I am getting following error; Program gmxcheck, VERSION 4.6.5 Source code file: /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c, line: 92 Fatal error: Magic Number Error in XTC fil