[gmx-users] POPC simulation

thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top & popc.itp

Re: [gmx-users] g_energy -fee -inf problem

Naser, Md Abu wrote: Hi All User, I am getting free energy difference -inf. 1st I run a protein in water molecule and then I made a different topology file with deleting 4 disulfide bonds and accordingly the angles and diherdal angles. What physical model are you trying to reproduce here? The

Re: [gmx-users] atom index number

Hi, With less than 10 atoms, making an index file from a gro file is easy with grep, cut and awk. Make a gro file with trjconv, then process it with aforementioned tools. /Erik 21 sep 2007 kl. 17.33 skrev Naser, Md Abu: Hi Gmx user, I have wondering whether it is possible to extract

[gmx-users] g_energy -fee -inf problem

Hi All User, I am getting free energy difference -inf. 1st I run a protein in water molecule and then I made a different topology file with deleting 4 disulfide bonds and accordingly the angles and diherdal angles. Then, I run -rerun for the both and and g_energy -fee, which giving me free energy