[gmx-users] Software inconsistency error: One or more interactions were multiple assigned in the domain decomposition

, -- Olivia Waring Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests

[gmx-users] Domain decomposition problems

Dear Gromacs users, Could someone please shed light on the following problem? My system consists of an alkanethiol SAM (in the xy plane) with a layer of water on top. The mdrun command works when the box vectors are 1.1, 1.3, and 2.5, but the SAM flies apart and the simulation crashes. I'm trying

Re: [gmx-users] Re: Generating Pairs with a Buckingham Potential

again, Olivia On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/12/11, *Olivia Waring *owar...@princeton.edu wrote: I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically

[gmx-users] (no subject)

1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post

[gmx-users] Re:

looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar

[gmx-users] Using tables to construct a z-dependent 12-3 potential

-- Olivia Waring Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests

Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential

: On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would

Re: [gmx-users] grompp: invalid bond type error

On Tue, Nov 1, 2011 at 8:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 2/11/2011 8:32 AM, Olivia Waring wrote: Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing

[gmx-users] grompp: invalid bond type error

The error is rather cryptic, and I'm having trouble tracking it down... I even went to the source code (topdirs.c), but I'm still not sure where exactly this invalid bond type is being defined. Thank you so much for your help, Olivia -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry

Re: [gmx-users] grompp: invalid bond type error

Does this help? Thanks so much again, Olivia On Tue, Nov 1, 2011 at 5:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Olivia Waring wrote: Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type

[gmx-users] Simulating an alkanethiol SAM on gold: atom type not recognized when running pdb2gmx

. M. W. -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un