[gmx-users] Question on checkpoint files and restarts/continuity

or is there a preferred method for doing something like this? Thanks in advance for any help you can provide. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://list

[gmx-users] Question regarding freeze groups and their use

imb.: force 2395.3% pme mesh/force 1.243" which I believe must be due to the frozen protein causing difficulties with domain decomposition. Can anyone offer any advice regarding these issues? I know this has been discussed often, but nothing I'm finding in the archives is particularly rel

[gmx-users] Updating charges on-the-fly

who has done a similar thing successfully and cares to share any tips or code. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham wrote: > On 6/09/2011 1:22 AM, J. Nathan Scott wrote: > > > > On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote: > >> On 5/09/2011 3:30 AM, J. Nathan Scott wrote: >> >>> Hello fellow GROMACS users, >>&g

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote: > On 5/09/2011 3:30 AM, J. Nathan Scott wrote: > >> Hello fellow GROMACS users, >> >> I am in the process of constructing a new residue in the OPLS-AA force >> field for the mCherry chromophore. However, I am havin

[gmx-users] Question about adding hydrogens to a newly constructed residue

s are OK, since they seemed to work fine before, as indicated by examining the gro file. I would sincerely appreciate any help you can offer. Thank you! -Nathan -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users

[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load)

Oops, this message and the original should have gone to the VMD mailing list and not Gromacs of course. My mistake, apologies for cluttering your inbox. :-) -Nathan On Thu, May 5, 2011 at 3:35 PM, J. Nathan Scott < scot...@chemistry.montana.edu> wrote: > Hello again, fellow gmx-use

[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load)

I'm hoping that there is some better way to do this that I haven't thought of yet. My script runs very wonderfully except for this chunk. Thanks in advance for any help you can provide, -Nathan On Wed, May 4, 2011 at 11:06 AM, J. Nathan Scott < scot...@chemistry.montana.edu>

[gmx-users] Trouble loading User data with a Tcl script (only half the data seems to load)

e for any advice you can provide. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University ### set first 0; set last 1000; set mut wt; set mut_ wt_; set

[gmx-users] Replacing a residue and continuing a simulation run

better way to do the sort of residue replacement I'm contemplating, or is this something that is just inherently going to be a bit messy? Thanks very much for any insight or guidance you can offer! -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and B

[gmx-users] Interatomic distance matrices

that could generate such matrices? This would not be hard to code, but time savers are always appreciated. :) Best Wishes, Nathan -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

On Thu, Dec 9, 2010 at 3:38 PM, Mark Abraham wrote: > On 10/12/2010 9:14 AM, J. Nathan Scott wrote: >> >> Hello gmx users! I realize this may be a touch off topic, but I am >> hoping that someone out there can offer some advice on how to build >> Gromacs for parallel

[gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

e tips or spot any obvious problems with my method that I have not noticed and would sincerely appreciate any help you can offer a novice. Best Wishes, -Nathan -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users

Re: [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?

On Tue, Dec 7, 2010 at 3:17 PM, Mark Abraham wrote: > On 8/12/2010 4:07 AM, J. Nathan Scott wrote: >> >> Hello all! I spent some time searching the archive and can't find an >> answer to this question. Is there a replacement for the -rtpo option >> for pdb2gmx? T

[gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?

ry, but this is clearly not the case. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

Re: [gmx-users] Trouble with Gromacs finding the files it needs

On Tue, Nov 30, 2010 at 2:13 PM, Justin A. Lemkul wrote: > > > J. Nathan Scott wrote: >> >> Hello Gromacs users, >> >> I am having some difficulties with Gromacs finding the files it needs >> (at least that is what I *think* is the problem) and am hoping

[gmx-users] Trouble with Gromacs finding the files it needs

igure --disable-float --prefix=/home/scott/gromacs --program-suffix=_d make && make install make distclean ./configure --enable-float --prefix=/home/scott/gromacs make && make install Thank you very much for any help you can provide, this problem really has me scrat

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 152

On Tue, Nov 23, 2010 at 9:55 AM, wrote: > J. Nathan Scott skrev 2010-11-23 17.35: >> Hello Gromacs users, >> >> I was wondering, have the AMBER 11 and/or AMOEBA force fields been >> implemented by anyone for use in Gromacs? The reason I ask is that we >> are very

[gmx-users] AMOEBA/AMBER 11 in Gromacs?

all possible. Thanks in advance for any insight you can provide. Best Wishes, -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx