[gmx-users] ERROR: Number of grid cells is zero

I am trying to do the NPT equilibration of a cyclic peptide in DMSO solvent BOX using all atom charm force field (ffcharmm27) on GROMACS. The NVT equilibration is working but the NPT equilibration shows the following ERROR. Back Off! I just backed up results/eq50K.log to results/#eq50K.log.1#

[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)

force field) > To: Discussion list for GROMACS users > Message-ID: <4dff88b9.4080...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 21/06/2011 2:44 AM, udaya kiran marelli wrote: > > Dear GROMACS users, > > > > I have gene

[gmx-users] NVT equilibration of DMSO solvent (Charmm all-atom force field)

Dear GROMACS users, I have generated a 4*4*4 octahedral DMSO box containing 64 molecules (Charmm all-atom force field) which need to be NVT equilibrated in order to pass it for usage in genbox. Could one of you provide info on how to do the NVT and periodic boundary equilibration to remove the re

Re: Re: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field

naging the list at >gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. cyclic peptide on GROMACS compatoble with Charmm

[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field

Dear GROMACS users, I am trying to construct a cyclic hexa peptide containing all Ala residues. During pdb2gmx conversion using the command(pdb2gmx -ff charmm27 -ignh -f TESTALA.pdb -o TESTALA.gro -ter) it gave the following error while I am demanding the program to give uncharged termini (