Re: [gmx-users] Umbrella sampling

Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- Gromacs Users mailing list * Please search

[gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

Hi there, g_membed is not able to fix the clashes while using the Amber force field, but when I use the gromos force field , it can fix the clashes and also It can insert the big protein onto the membrane perfectly. Thanks Ram -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

Thanks for the reply. For all-atom Amber ff, Should I change the neighbor list value or change in the cut-off for VdW interactions. As the side-chain hydrogen atoms might be clashing with the lipid atoms and thus producing many LINCS warning. Thanks Ram -- Gromacs Users mailing list * Please

Re: [gmx-users] Running on two nodes

Or May be you can keep the options as default. Then mdrun will automatically use all the resources available. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups?

r will select all atoms without hydrogens. ri will select all atoms including all hydrogens too. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] How to create a group for a set of atoms with make_ndx

Index file is always in a serial no. You can check the residue serial no. by opening the pdb in text format. "gmx make_ndx " is the command to use to see all indices and then choose your residues accordingly. -- Gromacs Users mailing list * Please search the archive at