[gmx-users] conversion of amber outputs to gromacs

Dear gromacs users I did md simulation of my system (protein+ligand) using amber. I want to do some analysis using gromacs. In gromacs, I need to xtc and top file for analysis. How do I convert mdcrd to xtc and prmtop to top files? I used AMBER 10 for doing MD simulation. I used amber03 force

Re: [gmx-users] extracting velocities

Hi Mah, g_traj -ov or use trjconv to write a .gro/.g96 with velocities. Cheers, Tsjerk On Dec 26, 2014 7:36 AM, "mah maz" wrote: > Dear all, > > What are the ways of extracting velocities from output files? I have used > g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are the

Re: [gmx-users] extracting velocities

Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah On Fri, Dec 26, 2014 at 10:05 AM, mah maz wrote: > Dear all, > > What are the ways of extracting velocities from output files? I have used >

Re: [gmx-users] extracting velocities

No, I meant -ov It writes the velocities for the selection. Cheers, Tsjerk On Dec 26, 2014 9:54 AM, "mah maz" wrote: > Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell > me the differences between -cv veloc.pdb and the mentioned command? > > Regards > ,Mah > > On Fri, D

Re: [gmx-users] MMPBSA & GMXPBSA 2.1

Hi Thomas, please forward your request to the GMXPBSA mailing list: https://groups.google.com/forum/#!forum/gmxpbsa probably it is a problem about the configuration Best and On 26/12/2014 08:57, Tom wrote: Dear GXM Users, Is there anyone who has the experience of GMXPBSA 2.1? I download

Re: [gmx-users] How to use gmx convert-tpr for GMX5.0.4

On Fri, Dec 26, 2014 at 4:33 AM, Smart Eagle wrote: > Hi all, >I can use tpbconv to restart or extend simulations for GMX 4.x version. > Now I have installed the newest verion of GMX 5.0.4, and I found the > tpbconv com‍mand had been changed into "gmx convert-tpr". But when I use > this gmx

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

Hi, The most likely explanation is that you were using a network file system that dropped out for some time, was later restored, and it lost some data in the meantime. This might happen if it was caching data before writing it to disk, telling mdrun everything was OK, and something traumatic happe

[gmx-users] Umbrella sampling along a dihedral angle

Dear Gromacs community, Using enforced rotation potentials I have generated a really smooth rotation of my ligand the catalytic binding domain of my protein. I then put together a simple perl script to calculate the dihedral angle of four particular atoms at each time step using g_angle. Taking

Re: [gmx-users] extracting velocities

Hi Tsjerk Got the point. It worked; thanks alot! Regards, Mah On Fri, Dec 26, 2014 at 12:23 PM, mah maz wrote: > Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell > me the differences between -cv veloc.pdb and the mentioned command? > > Regards > ,Mah > > On Fri, Dec 26

[gmx-users] How to plot a droplet radius profile as a function of z-direction?

Dear gmx-users, Q1) I would like to plot the radius profile of a water droplet on graphene, as a function of z-direction, as per below:http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/largeWhich GROAMCS utility should I use, and how do I go about plotting the profile?Q2)