Re: [gmx-users] μVT simulations and genbox

In theory, https://github.com/GromPy/GromPy can do it (http://www.ncbi.nlm.nih.gov/pubmed/22370965), but it's old and I've never tried it. Not in the main code currently. On Wed, Feb 10, 2016 at 11:38 AM, Irem Altan wrote: > Hi, > > I have two questions: > > - Is it

[gmx-users] improper dihedral convention

Dear All: I want to apply OPLS-UA improper dihedral to fused benzene ring. I am confused with sequence of atoms. I went through manual 4.6.7,page 79, I have confusion. * l* | | * i* / \ /\

[gmx-users] μVT simulations and genbox

Hi, I have two questions: - Is it possible to do μVT simulations? - When I copy vdwradii.dat to my working folder and modify it, does it affect the MD simulations? I used it to modify the number of water molecules genbox adds, and then ran an MD simulation without removing the vdwradii.dat

[gmx-users] Reading multiple trajectories for Gromacs analysis

Hello all, I just finished a 100 ns simulation using Gromacs, where I ran the simulation with a 5 ns window (ie. now I have 20 .trr files with 5 ns data in each). As I am quiet new to Gromacs, I just wonder how can I read all the 20 trr files one-by-one to do some basic Gromacs analysis. For e.g

Re: [gmx-users] improper dihedral convention

Hi, Yes, the image seems to have been cropped poorly somehow. Hopefully I can fix it. I is an the middle and j is in the bottom left - if you zoom in the pdf you can see that only one of the letters i has a serif on the bottom. Mark On Wed, 10 Feb 2016 18:41 Parvez Mh

[gmx-users] Weird configuration when pulling rate is small

Dear list, I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow away from the triple helix), but the simulations

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Dear Mark, Please find attached a plot showing the RMSD difference. It is for the same protein. Even if the same runs are not reproducible, my doubt is whether there can be such a large variation in the RMSD trend. Which data should I rely on then, it is giving me a hard time. I'll be grateful

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Hi Sapna, The list doesn't allow attachments. Please put them somewhere online and provide a link. The differences can be large. Can't tell if you don't know the possible range of conformations/trajectories for one Gromacs version. Did you ensure to remove jumps from the trajectories and/or make

Re: [gmx-users] Gromacs installation FTP issue

Hi, Yes, you could have simply changed the ftp:// prefix to http:// and it would have been fine. Future releases will likely offer both styles of link. The regressiontest download is only available with http for now, so your problem there was not related to FTP limitations. Mark On Wed, Feb 10,

Re: [gmx-users] complex topology file

please someone help me. i want to find out absolute binding free energy of protein ligand complex. fisrt i performed docking and selected best poses and then i made topology file of ligand with PRODRGserver. and then included itp file of ligand in Protein topology file (from pdb2gmx) , also

Re: [gmx-users] complex topology file

On 2/10/16 8:34 PM, Sana Saeed wrote: please someone help me. i want to find out absolute binding free energy of protein ligand complex. fisrt i performed docking and selected best poses and then i made topology file of ligand with PRODRGserver. and then included itp file of ligand in Protein