[gmx-users] Terminus Atoms genrestr?

doing this I would be very happy.   Thank you, TJ Mustard -- 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

Re: [gmx-users] Terminus Atoms genrestr?

es by specifying them with the argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to make a positional restrain file via makerestr. I am just hoping there is a better, more automated way of doing this.     Thank you, TJ Mustard On February 11, 2011 at 10:

Re: [gmx-users] Terminus Atoms genrestr?

Justin,   Ok, if I find a way I will post it back here. And thank you for the recommendations.   Thank you, TJ Mustard On February 11, 2011 at 11:05 AM "Justin A. Lemkul" wrote: > > &g

[gmx-users] FEP energy errors with positional restraints?

n to "normal" levels.   Does anyone have an idea what is happening? And if you do, can you please give a recommendation? Thank you, TJ Mustard musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

Re: [gmx-users] FEP energy errors with positional restraints?

  On February 12, 2011 at 5:35 PM Mark Abraham wrote: On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all,   I have been testing the ability of taking a sphere of a protein around a ligand, and

Re: [gmx-users] Output of Gromacs Demo

Yahoo! Mail Q&A for great tips from Yahoo! Answers users.   TJ Mustard Email: musta...@onid.orst.edu -- 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/M

Re: [gmx-users] FEP energy errors with positional restraints?

  On February 12, 2011 at 9:31 PM Mark Abraham wrote: On 13/02/2011 3:57 PM, TJ Mustard wrote:   On February 12, 2011 at 5:35 PM Mark Abraham wrote

Re: [gmx-users] FEP energy errors with positional restraints?

  On February 12, 2011 at 10:14 PM Mark Abraham wrote: On 13/02/2011 5:03 PM, TJ Mustard wrote:   On February 12, 2011 at 9:31 PM Mark Abraham wrote

Re: [gmx-users] free energy

ystem and setting I am using. Thanks Moeed   TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

Re: [gmx-users] free energy

ett's Acceptance Ratio? This make for a little more work but knowledge of your error is nice.   Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed   TJ Mustard Em

[gmx-users] Re: free energy

small number of lambda values you will want to use more.   Please email me with questions if you need more.   Thank you, TJ Mustard Email: musta...@onid.orst.edu     PS more below On February 14, 2011 at 8:54 PM

Re: [gmx-users] GAUSSIAN Error message

e for BuckyBall  0  3 You have a no charge triplet? Is this a carbene?   TJ Mustard C    -0.677394    -0.928398    -3.166238 C    0.672998    -0.928446    -3.166308 C    1.090287    0.355662    -3.166349

Re: [gmx-users] GAUSSIAN Error message

> You may try "dos2unix" > > On Thu, Feb 24, 2011 at 8:07 PM, Sergio Manzetti > wrote: > > No. It contains a charged Gandolinium ion in the middle of a buckyball. > > > > > > > > On Fri, Feb 25, 20

[gmx-users] Getting some interesting errors.

nk you for any assistance, TJ Mustard Email: musta...@onid.orst.edu -- 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

RE: [gmx-users] Getting some interesting errors.

Yes "-dlb no" not on and I will file a bugzilla. Thanks again Berg Hess.   TJ Mustard On September 20, 2010 at 8:38 PM Berk Hess wrote: Hi, Could you file a bugzilla? And what do you

Re: [gmx-users] Getting started - Peptide

g! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >   TJ Mustard Email: musta...@onid.orst.e

[gmx-users] Psuedo ONIOM gromacs MD run

ement artifacts.   Thank you,   TJ Mustard Email: musta...@onid.orst.edu -- 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

Re: [gmx-users] Psuedo ONIOM gromacs MD run

- Original Message - From: TJ Mustard Date: Tuesday, September 28, 2010 10:46 Subject: [gmx-users] Psuedo ONIOM gromacs MD run To: "gmx-users@gromac

[gmx-users] Another error that keeps comming up.

onds   Any help would be appreciated. It also seems to be intermittent as I have 21 identical runs (with different lambda values) and some work and some don't. It also changes every time I run them. Thank you, TJ Mustard Email: musta...@onid.orst.edu -- gmx-u

Re: [gmx-users] Another error that keeps comming up.

Found that if I set the setting of "-dlb no" when running the mdrun it would not fail. How could dynamic load balancing do this?   TJ Mustard   On September 28, 2010 at 3:21 AM TJ Mustard wrote:

Re: [gmx-users] Another error that keeps comming up.

ll save the next guy some heartache and precious time.   Thank you again,   TJ Mustard   Roland On Tue, Sep 28, 2010 at 12:54 PM, TJ Mustard <musta.

[gmx-users] Is there a setting for defualt genion selection?

Hello all,   Is there a argument that will select SOL as the defualt selection for ion substitution? I read the manual and found nothing.   Thank you, TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Is there a setting for defualt genion selection?

On October 1, 2010 at 7:16 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Hello all, > > > >  > > > > Is there a argument th

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

rg/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >   TJ

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

lues. Also make sure you name your couple-moltype correctly. If you use "lig" use lig for your couple-moltype. It will most likely fail if you set it up wrong. Also the manual explains these settings, so you can understand what they do.   Thank you, TJ Mustard   Yo

Re: [gmx-users] problem of paralleled running

without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure. All the best, fancy     TJ Mustard

Re: [gmx-users] problem of paralleled running

On October 28, 2010 at 4:11 AM TJ Mustard wrote: On October 28, 2010 at 4:05 AM fancy2012 wrote: Dear GMX users

[gmx-users] When will FEP be on GPU?

be happy to be a/the guinea pig on this one.   Thank you, TJ Mustard Email: musta...@onid.orst.edu -- 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

Re: [gmx-users] free energy of methan disappearing:tutorial

of my questions Thank in advance for your reply Sincerely yours Mohsen   TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

Re: [gmx-users] adding Na and cl ions to pdb structure

pdb file which contains my protein and one Na and one Cl ion. by pymol?How? by manipulating pdb file?How? Thanks in advance   TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Energy minimization query

.   Hope this helps, TJ Mustard On December 28, 2010 at 8:26 AM nikhil damle wrote: Hi, I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly

[gmx-users] Allitle stumped about FEP, and my setup for calculating energies...

this answer) How precise is enough? (standard deviations of less than 2 kJ/mol in BAR?) Currently we are running long (2.5ns) relaxation MDs with no FEP and then running FEP on them for various times, hoping this will decrease any errors we are seeing. Thank you, TJ

[gmx-users] Speed up my jobs with PME and grid spacing?

Hi,   I am trying to speed up my parallel processor Gromacs jobs and was wondering what were the known settings for PME cut-off and PME grid spacing? As of now I am running with a PME cutoff of 0.8 and a fourierspacing of 0.12.  Thank you, TJ Mustard

[gmx-users] Segmentation Fault in EM

ot; energy minimization.  This happens on our cluster and on our iMacs.   Any help would be appreciated. Also I can attach my mdp files.   Thank you   TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

[gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

.   The jobs will continue on and finish but we are worried about the error that could be included with these errors.     Any help would be appreciated. Also I can attach my mdp files.   Thank you, TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing

Re: [gmx-users] Segmentation Fault in EM

  On January 17, 2011 at 1:20 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Hi all, > > > >  > > > > I have be

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

No this is a completely different error that occurs when the other (EM) error does not.   Thank you, TJ Mustard On January 17, 2011 at 1:51 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > &g

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

  On January 17, 2011 at 2:15 PM TJ Mustard wrote: No this is a completely different error that occurs when the other (EM) error does not.   Thank you, TJ Mustard On January 17, 2011

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

  On January 17, 2011 at 2:21 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > No this is a completely different error that occurs when the other (EM) > > error

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

.   I have also had this issue in our scripts before and I made sure to fix and check all others at that time.     Thank you though, TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

  On January 17, 2011 at 2:47 PM TJ Mustard wrote:   On January 17, 2011 at 2:21 PM "Justin A. Lemkul" wrote: > > &g

Re: [gmx-users] table-extension in mdp ?!

re than I. If I were you I would fix the two "NOTES" first. Once those go away the 1-4 interaction warning might disappear as well.   TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

  On January 17, 2011 at 3:48 PM Mark Abraham wrote: On 18/01/2011 10:27 AM, TJ Mustard wrote:   On January 17, 2011 at 2:47 PM TJ Mustard wrote

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

  On January 18, 2011 at 12:50 PM Mark Abraham wrote: On 19/01/2011 7:33 AM, TJ Mustard wrote:   On January 17, 2011 at 3:48 PM Mark Abraham wrote

[gmx-users] Two machines, same job, one fails

ep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg     I can add my .mdps but I do not think they are the problem since I know it works on my personal iMac.   Thank you, TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-

Re: [gmx-users] Two machines, same job, one fails

  On January 25, 2011 at 2:08 PM Mark Abraham wrote: On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all,   I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2

Re: [gmx-users] Two machines, same job, one fails

  On January 25, 2011 at 3:24 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > >  > > > > > > On January 25, 2011 at 2:08 PM Mark Abraham

Re: [gmx-users] Two machines, same job, one fails

  On January 25, 2011 at 3:54 PM Mark Abraham wrote: On 01/26/11, TJ Mustard wrote

Re: [gmx-users] Two machines, same job, one fails

  On January 25, 2011 at 3:53 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > >  > 1. Do the systems in question crash immediately (i.e., step zero) or >

Re: [gmx-users] Re: free energy calculation , grompp crash

Dawei,   I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?   Thank you, TJ Mustard  On February 7, 2011 at 9:31 AM Da-Wei Li wrote: Well. It  actually isn&#

Re: [gmx-users] Re: free energy calculation , grompp crash

Da-Wei, Do you need FEP information on the PR step? Are you going to do a MD(sd) with FEP on after the PR?   And are you doing hydration of a protein?   Thank you,  TJ Mustard On February 7, 2011 at 10:23 AM "Jus

Re: [gmx-users] Re: free energy calculation , grompp crash

dawei On Mon, Feb 7, 2011 at 1:31 PM, TJ Mustard <musta...@onid.orst.edu> wrote: Da-Wei, Do you need FEP information on t

[gmx-users] Anealling

ints on my ligand and protein, what I wish to know is if this will cause artifacts in my system? Thank you, TJ Mustard musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

Re: [gmx-users] PRODRG

cs.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 to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Ca

[gmx-users] Amber force fields giving LINCS errors

.     Thank you in advance,   TJ Mustard Email: musta...@onid.orst.edu Cell: 509-879-4173   -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Amber force fields giving LINCS errors

atoms 6545 and 6542) bonds that rotated more than 30 degrees:  atom 1 atom 2  angle  previous, current, constraint length       I hope this is enough information (and not to lengthy). Any help would be much appreciated.      

Re: [gmx-users] Amber force fields giving LINCS errors

My one thought is that it is to large of a system for GROMACS to run it, yet I have run a small protein in GROMOS96-43a1 and it works but not in any of the AMBER force fields. On September 9, 2010 at 9:35 PM TJ Mustard wrote: Of

Re: [gmx-users] Amber force fields giving LINCS errors

On September 9, 2010 at 10:04 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > *Positional restraint mdp file:* > > > >  &g

[gmx-users] PDB will not minimize?

uot;_md.tpr -o "$base"_md.trr -c "$base"_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt I NEVER get to here     I have stripped the MG and ZN. I have removed a significant portion of the protein/rna to limit its size. I have ran

Re: [gmx-users] PDB will not minimize?

  My appologies I have errors all over this. On September 11, 2010 at 12:44 AM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Downloaded a

[gmx-users] FEP top file setup...

k you in advance,   TJ Mustard Email: musta...@onid.orst.edu -- 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'

Re: [gmx-users] FEP top file setup...

- From: TJ Mustard Date: Tuesday, September 14, 2010 10:54 Subject: [gmx-users] FEP top file setup... To: "gmx-users@gromacs.org"     >

[gmx-users] Has anyone seen this error befor?

I have searched for this on google and found nothing. Do I need an Improper Dihedral section in my top/itp file? I have ran this same system with fep off and it runs perfectly.   Any help is much appreciated.   TJ Mustard Email: musta...@onid.orst.edu -- gmx-use

Re: [gmx-users] Has anyone seen this error befor?

Thank you both.   I have set up soft core parameters for this test. All I want is an actual test to work at this point. On September 15, 2010 at 5:31 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > &