Re: [gmx-users] ATP for

rface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ---------- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

[gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

enough so that this bond is not being applied across the boundary. Otherwise someone else may have more ideas to help you. Tom Forwarded Message Date: Wednesday, January 06, 2010 22:43:20 +0100 From: Hans HEINDL To: TJ Piggot Cc: Subject: simulationg a distance

Re: [gmx-users] define a new covalent bond in gromacs

mx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php --------

Re: [gmx-users] get 3 roation angles over time

e search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- TJ Piggo

Re: [gmx-users] For FFamber, should FudgeLJ variable in ffamber.itp be 0.0?

ad http://www.gromacs.org/mailing_lists/users.php ------ TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/sear

RE: [gmx-users] Pushing MD further

yourself instantly with MSN Messenger! MSN Messenger -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!

Re: [gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

Re: [gmx-users] Urea Topology

27;t post? Read http://www.gromacs.org/mailing_lists/users.php ---------- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search be

RE: [gmx-users] trjcat xtc files

gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 h

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] trjconv to process multiple types of molecules

archive at http://www.gromacs.org/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/mailing_lists/users.php ------ TJ Pi

Re: [gmx-users] Z-position calculation

e the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ------ TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing list

Re: [gmx-users] analyzing gromacs trajectories on VMD

analyze the gromacs trajectories using vmd, is there a quick way of doing so ? Is there a reference for this? Thank you Amit  -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users

Re: [gmx-users] make_ndx help

an/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ---

Re: [gmx-users] Gromacs in Parallel

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/mailing_lists/users.php ------ TJ Piggot t.pig...@bristol.ac.uk University

Re: [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx

ead http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Problems with Jacobi diagonalization

www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search befor

Re: [gmx-users] Triclinic water box for a protein MD

to be submitted. Unfortunately I haven't had time to dig into the GMX 4 code to implement the rotational constraints yet. I wouldn't want to compromise the performance :S Cheers, Tsjerk On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot wrote: You might want to try a rombic dodecahedron box

Re: [gmx-users] Triclinic water box for a protein MD

cs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/us

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

Sorry realised I posted the amber ATP link wrong, it is without the ) at the end: http://www.pharmacy.manchester.ac.uk/bryce/amber Tom --On Thursday, February 26, 2009 17:15:22 + TJ Piggot wrote: Some of these charges look a bit suspect to me (eg the charge on the gamma phosphate

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

ace or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://w

Re: [gmx-users] eigenvalues

Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] Analyzing a trajectory split over multiple files

pt to do this kind of stuff, though. Nicolas Thank you very much! I always knew there must be something smart to be done. I should now delve into the nitty-gritty of scripting. grep seems to be a particularly useful tool! :) Regards, Suman. -- TJ Piggot [EMAIL P

Re: [gmx-users] doubt about the oplsaa topology

s to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing lis

Re: [gmx-users] which force field for a protein-protein complex?

oom 401 Bis Web Site: http://www.dsimb.inserm.fr/ ------ TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Parameters for DNA bases

Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Dealing with residues not in the topology database

n't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arc

Re: [gmx-users] TEE-REX installation error

! Tom --On Tuesday, June 10, 2008 02:14:40 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: TJ Piggot wrote: Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/

[gmx-users] TEE-REX installation error

me/tp1821/Gromacs/gromacs-3.3.1-teerex/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src' make: *** [all-recursive] Error 1 I am using the gcc 3.4.6 compiler on a CentOS 4 linux box and also gromacs 3.3.1 without the

Re: [gmx-users] GTP topology generation in OPLS-AA force field

on't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. _

Re: [gmx-users] how to calculate redisue wise RMSD in gromacs?

search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTE

Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?

://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. _

Re: [gmx-users] selecting residues which are within cutoff distances

ity of Denmark Copenhagen ------ TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.groma

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

as my biggest problem. I simply changed to a triclinic box without too much cost. However I think I could grab an extra 300ps/day if I had an actual fix. Cheers Mitch TJ Piggot wrote: I agree with increasing the size of the box (if seeing inconsistent shifts, as i should have mentioned in my previou

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

413 1 0 1 8.18 8.18 10.0 1.0 Have you defined the low up and up2 in the correct units? Cheers Mitch TJ Piggot wrote: Hi, Firstly I would strongly reiterate what Mark said. I would make sure the distance restraints are causing your problem. Again as Mark sai

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

Re: [gmx-users] DNA adduct simulation: grompp error

man/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -----

Re: [gmx-users] AMBER ff99SB port problems

acs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

Re: [gmx-users] problems with opls_

quests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing li

Re: [gmx-users] simulating hydrocarbons in water

e www interface or send it to [EMAIL PROTECTED] . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

number of mails in your inbox. Click here. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] about md simulation

;t post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ---------- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ g

[gmx-users] Re: \\[gmx\\-users\\] The energy minimization\\.\\.\\.\\.

n water) to test the topology in the GROMOS96 ff and it works fine for me, so there must > be a problem in one of your setup steps or your simulation > > parameters. Tom -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. -

[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)

Hi Also please keep emails on the list, it helps everyone (you getting more people's opinion than just mine, and people who may have a similar problem in the future) Tom Forwarded Message Date: 18 August 2007 02:29 +0100 From: TJ Piggot <[EMAIL PROTEC

Re: [gmx-users] Step size too small

fore posting! Please don't post (un)subscribe requests to the list. Use the  www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ------ TJ Piggot [EMAIL PROTECTED] Uni

Re: [gmx-users] The energy minimization....

r equilibrate these structures on their own, and now I suggest doing them also in solvent. This will help you eliminate sources of problems and guide you to what the real problem is. Divide and conquer... That's fine, then. OK, so here's your problem. Work out what's breaking and

Re: [gmx-users] Re:

acs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTE

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

CTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] Implicit solvent simulation

paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following

Re: [gmx-users] Implicit solvent simulation

s.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ------ TJ Piggot [EMAIL PROTECT

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

earch before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. _

Re: [gmx-users] which tool to use a measure a user-defined angle in a traj

users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ------ TJ Piggot [

Re: [gmx-users] g_bundle!

gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://ww

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

bscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-us

Re: [gmx-users] protein-DNA simulation with Amber port

Figured it out was just being a bit slow. I hadn't include an #ifdef _FF_AMBER statement in spce.itp or spc.itp Thanks Erik and Mark Tom --On Friday, June 01, 2007 23:35:22 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: TJ Piggot wrote: Hi I have just checked again by trying

Re: [gmx-users] protein-DNA simulation with Amber port

[ molecules ] section in correctly ordered. 1 jun 2007 kl. 14.55 skrev TJ Piggot: Hi, If i remember correctly i also got this error with spc (and spc/e) and the ffamber port. However i was only playing around in testing different water models and did not spend ages trying to fix this problem because

Re: [gmx-users] protein-DNA simulation with Amber port

LENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. -- TJ

Re: [gmx-users] Question about MD simulation

ys to rename those atoms (either in NT or amber files)? Thank you very much! Bo -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list

Re: [gmx-users] pdb2gmx error

CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Shape Yahoo! in your own image. Join our Network Research Panel today! -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK.

Re: [gmx-users] Problems using grompp and amber force field

Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Problems using grompp and amber force field

rg/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ---

Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

Hi I see what you are saying, i will try and recompile with the changes you have suggested Thanks you Tom --On Tuesday, March 06, 2007 14:07:36 +0100 Berk Hess <[EMAIL PROTECTED]> wrote: From: TJ Piggot <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To

Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK.

Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

d it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

[gmx-users] Inconsistent shifts using multiple bonds type 6

replace the problem 'bonds' in the topology file. Thanks for any advice you can give Tom Piggot ------ TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

Re: [gmx-users] opls parameters

or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

Re: [gmx-users] opls parameters

.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTE

[gmx-users] OPLS-AA Charge Calculation

. Thanks for any input you have on this approach Tom Piggot -- TJ Piggot [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques

Re: [gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

all molecular in its active site. But unfortunately, pdb2gmx cannot generate the gro and top file for the small molecualr? I am using the oplsaa force field, who can tell me how to generate the gro and top files? Thanks a lot Jian ---------- TJ Piggot

Re: [gmx-users] Hi

ology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- TJ Piggot [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www