[gmx-users] how to remove water molecule inside micelle?

Dear gromacs users I prepared my simulation system containing SDS. Then I added water molecules using genbox. Some water molecules entered in to the micelle. How to remove water molecules inside the micelle? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the a

[gmx-users] charge distribution

Dear Justin i really appricite for your help i want to tell all did work until now, again: 1.total charges in my topol.top was +2, then by genion, i added 2 CL to my comlex (HSA+Aspirin) 2.My .itp file (produce by PRODRG) was(consist of 11 atoms) : [ moleculetype ] ; Name nrexcl SAL 3 [ a

[gmx-users] Fatal error during entropy calculation using g_anaeig

Hi all, I am trying to calculate entropy using g_anaeig (Gromacs version 5.0.1), after using g_nmeig to calculate eigenvectors and eigenvalues (after computing hessian matrix): g_nmeig_mpi -f hessian.mtx -s run.tpr -nom g_anaeig_mpi -v eigenvec.trr -entropy But I am getting the following error:

Re: [gmx-users] Umbrella sampling along a dihedral angle

Hi Justin, Thanks for the reply, always appreciated. I like the way gromacs can handle modular structures by breaking up the topology into separate .itp file. Unfortunately this is the first time I've had to span two subunits with a specific restraint. I quickly knocked together a perl script t

Re: [gmx-users] core dumped

On 12/27/14 4:22 PM, elham tazikeh wrote: Dear Justin thanks for your advise only my remained question is, if my problem was for my topology file (as i recieved this error a few times: your topology file has non-zero charge = -0.61) by editing my topology file (.itp file), can i going on

Re: [gmx-users] charge distribution

On 12/27/14 3:54 PM, elham tazikeh wrote: Dear gromacs users i d like to know about charge distribution in .itp file that how can fix the charge of atoms for instance, i simulated Aspirin in Human serum albumin, and i want to know about their charges in an article charge distribution was as bel

Re: [gmx-users] Umbrella sampling along a dihedral angle

On 12/27/14 1:50 PM, Nash, Anthony wrote: Hi Justin, I think I've shot myself in the foot and I'm trawling the gromacs manual with little success at the moment. I'm trying to define my [ dihedral_restraint ] over my ligand-enzyme complex. The topology of the ligand is in one .itp file and t