Re: [gmx-users] visualizing more than 9999 residues....

nstitute for Advanced Materials > University of Groningen > The Netherlands > -- > 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! >

Re: [gmx-users] gromacs on glacier.westgrid.ca

Hello Payman, Westgrid (and Glacier) has several pages of doc on its website about running Gromacs and compiling softwares. I used to run (my own compilation of) Gromacs on Glacier and never had any particular problem. You just have to make sure you compile it with the correct mpicc and fftw

Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

Shay Amram a écrit : Dear GROMACS users, I have been trying to expand a membrane by a non-integer multiplier (for example X1.5). This can be done using *genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z*** This has worked very good with _homogenous_ membranes, and only ver

Re: [gmx-users] GMX Installation

terface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44 ___

Re: [gmx-users] waters in ion channels

o highlights and > more. Click here > http://cricket.yahoo.com___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the ar

Re: [gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)

_lists/users.php >> >> >> >> -- >> >> ___ >> gmx-users mailing list >> gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search

Re: [gmx-users] GROMACS to AMBER

> 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 -- [ Nicolas S

Re: [gmx-users] charmm c36 lipids

*** >>> >> >> >> >>> 3 sep 2010 kl. 20.56 skrev Drew Bennett: >>> >>>> Dear Pr Bjelkmar, >>>> >>>> I saw on the gromacs mailing list that you have python a script for >>>> converting CHARMM ff to GM

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Hello Thomas, I have a tcl script in my personal script library that might do what you want to do. I didn't use it for quite a while, but it was working well as far as I remember. I think it has been adapted from a script available on the VMD website, but I don't remember exactly its history.

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

e if one work with VMD. You store at once, bonds, atom types and charges. Actually, I should have somewhere a .rtf file for the Martini amino acids and lipids (the equivalent of the Gromacs rtp file for CHARMM). It can be used by psfgen to generate a psf file with Martini bonds, charges and atom typ

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

coarse_grain.tcl: line 25: global: command not found > : command not found line 26: > : command not found line 41: > : command not found line 45: > ./coarse_grain.tcl: line 120: syntax error near unexpected token `}' > '/coarse_grain.tcl: line 120: ` } else { > > b

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

ain.tcl: line 120: syntax error near unexpected token `}' '/coarse_grain.tcl: line 120: ` } else { best wishes, Baofu Qiao Nicolas SAPAY wrote: Justin A. Lemkul wrote: I have also added a Perl script to the GROMACS site (the VMD page): http://www.gromacs.org/Devel

Re: [gmx-users] Docking with PyMol and using Gromacs

Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presenc

Re: [gmx-users] vmd does not display the molecule

Hello, Did you try to just add a blank line at the end of the file? (after the box definition). Sometimes, that works for me. Otherwise, it could a problem of bad end-of-line character. That may happen if you have edited the file on Windows and try to visualize it on Linux. Nicolas leila ka

Re: [gmx-users] "coarse_grain.tcl" script does not show all of the coarse-grained bonds in vmd

Ozge Engin a écrit : Hi all, I was trying to show the bonds between my CG beads in VMD. I have four CG beads per each molecule, and there are 18 separate molecules which contain these four beads, which results in having 72 CG beads in total. Therefore, I expect to see 54 CG bonds in the

Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen

Re: [gmx-users] CHARMM to Gromacs

I add a similar problem a while ago. Unfortunately, I don't remember well what I have done to fix it. I think it was a stupid format problems like a blank line. I think I sent a message to mailing-list about that, without specifying it was for CHARMM, though. Here is my own version of NH3+ whic

Re: [gmx-users] CHARMM FF

Sorry for the late answer. I wasn't in my office on the last 2 weeks. Roland Schulz wrote: On Thu, Jul 17, 2008 at 6:26 PM, Nicolas <[EMAIL PROTECTED] > wrote: We also have a implementation of CHARMM(27) for Gromacs, but without CMAP as well. How is it d

[gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1 FAILED. Check files in rb1 And two complex tests failed as wel

Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Nicolas Sapay wrote: Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >mdrun.out 2>&1 FAILED. Check files in r

Re: [gmx-users] rb1 test failed after recompiling gromacs 3.3.2

Justin A. Lemkul wrote: Nicolas Sapay wrote: Nicolas Sapay wrote: Hello, I've run the gmxtest on Gromacs-3.3.2. One simple test failed: Testing rb1 . . . *** glibc detected *** realloc(): invalid next size: 0x082c0180 *** sh: line 1: 27398 Aborted mdrun >m

Re: [gmx-users] How to display simulation box in VMD?

You should have a look in the archives of the VMD mailing-list... Or check this page: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcbox/ Nicolas Suman Chakrabarty wrote: How do I display the actual simulation box in VMD for a gromacs configuration/trajectory? Is it possible? By

Re: [gmx-users] Coul-SR:SOL-SOL

Justin A. Lemkul wrote: Vitaly Chaban wrote: Thank you very much! So what energy is described by Coul-SR:SOL-SOL? And by LJ-SR? Lennard-Jones-short range..? What is it? I'm not 100% sure, as I've never had a need to break down energy terms in this level of detail, personally. My guess wo

Re: [gmx-users] Coul-SR:SOL-SOL

Nicolas Sapay wrote: Justin A. Lemkul wrote: Vitaly Chaban wrote: Thank you very much! So what energy is described by Coul-SR:SOL-SOL? And by LJ-SR? Lennard-Jones-short range..? What is it? I'm not 100% sure, as I've never had a need to break down energy terms in this level

[gmx-users] A MPI librabry not recognized by the configure script

Hi, I'm trying to compile the Gromacs-3.3.3 package with MPI and have the following issue when I run the configuration script: ./configure --prefix /home/users/nsapay/local/bin/gromacs-3.3.3 --program-suffix _mpi --enable-mpi --disable-nice MPICC=mpicc CC=gcc --without-x CPPFLAGS=-

Re: [gmx-users] A MPI librabry not recognized by the configure script

David van der Spoel wrote: Nicolas Sapay wrote: Hi, I'm trying to compile the Gromacs-3.3.3 package with MPI and have the following issue when I run the configuration script: ./configure --prefix /home/users/nsapay/local/bin/gromacs-3.3.3 --program-suffix _mpi --enable-mpi --di

Re: [gmx-users] A MPI librabry not recognized by the configure script

David van der Spoel wrote: Nicolas Sapay wrote: David van der Spoel wrote: Nicolas Sapay wrote: Hi, I'm trying to compile the Gromacs-3.3.3 package with MPI and have the following issue when I run the configuration script: ./configure --prefix /home/users/nsapay/local/bin/gromacs-

Re: [gmx-users] A MPI librabry not recognized by the configure script

David van der Spoel wrote: Nicolas Sapay wrote: David van der Spoel wrote: Nicolas Sapay wrote: David van der Spoel wrote: Nicolas Sapay wrote: Hi, I'm trying to compile the Gromacs-3.3.3 package with MPI and have the following issue when I run the configuration script: ./conf

Re: [gmx-users] still system exploid

Morteza Khabiri wrote: Dear gmxuser, Thanks for your all helps. But still I have problem. As you friend said I increase the vdw and box size and also i decrease the time step till 0.0001 but unfortunately system crash befor EM running. I do check with ngmx. To reply the question that said what

Re: [gmx-users] Leaflet of Bilayer

Justin A. Lemkul wrote: minnale wrote: Hi Jochen thanks for your reply I have gone through this recent mail http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html more over if I use genconf command like this genconf -f .gro -o out -nbox 2 1 1 -dist 0 0 0 its adding 128 in

Re: [gmx-users] Re: Leaflet of Bilayer

minnale wrote: Thanks Justin and Nicolas for gave suggestions. I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this [atomselect top "name P8 and z>0"] num it has showed 201, means the t

Re: [gmx-users] Re: Leaflet of Bilayer

Nicolas Sapay wrote: minnale wrote: Thanks Justin and Nicolas for gave suggestions. I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this [atomselect top "name P8 and z>0"

Re: [gmx-users] Topology files for OPLSAA and RESP charges

Hello, I just read your message... As far as I know, the RESP charge method is mainly employed forthe AMBER force field and associated (GLYCAM, GAFF, etc). I would check first that RESP is compatible with the method employed to develop OPLS-AA. Note that the AmberTools provide some scripts to

[gmx-users] Regular vs. CHARMM TIP3P water model

= md dt = 0.002 nsteps = 20 comm_mode= Linear nstcomm = 1 comm_grps= System -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 0

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

acs.org >> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model >> >> On 2010-09-14 10.23, Nicolas SAPAY wrote: >> > Hello everybody, >> > >> > I have many difficulties to reproduce TIP3P simulation results with >> CHARMM >>

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

g/doi/full/10.1021/ct900549r > gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched > from 1 to 1.2 nm). > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion > correction. > These numbers are quite different. I'll do some checking. > > Ber

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

is with LJ switched > from 1 to 1.2 nm). > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion > correction. > These numbers are quite different. I'll do some checking. > > Berk > >> Date: Tue, 14 Sep 2010 11:00:55 +0200 >> From: sp...@xray.bmc.u

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

gt;> does >> > not have to be identical. >> > The Gromacs Charmm FF implementation paper: >> > http://pubs.acs.org/doi/full/10.1021/ct900549r >> > gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ >> switched >> > from 1 to 1

[gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

d to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (40

Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

ZN2 ZN 1 0.2 CYSZZN2 (previsously : CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2) Supposing that "4" means "create 4 bond with", but nothing change. Any suggestion are welcomed! Thanks Nicolas David van der Spoel wr

Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

the inconvenience Nicolas Nicolas Sapay wrote: Thnaks for your answer, I have solved the problem with the lacking CD1 atom. There was a weid end of line the line jus before. But pdb2gmx is still unable to link correctly the ZN2 residue with the 4 CYS. The distance between SG and ZN atoms are

[gmx-users] problem with the max number of atom in charge group

042? Would it be a problem if I use PME? Note that the net charge of the molecule is still zero, of course. Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403

[gmx-users] OpenMosix and Gromacs

now. Additionally, I have already used sucessfully NAMD and OpenMosix (but NAMD uses its own tool for parallel process). Thanks Nico -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax

Re: [gmx-users] OpenMosix and Gromacs

d the Mosix userland tools and some other key functionality still don't work for 2.6 linux kernels. Nicolas Sapay wrote: Hi everybody, I wonder if someone has some experience with Gromacs and OpenMosix. Has someone tried recently to run Gromacs in parallel with an OpenMosix cluster? I have

Re: [gmx-users] OpenMosix and Gromacs

ning for sufficient amount of time for OpenMosix to migrate. 5) Next-generation software to come out... Regards, Yang Ye On 6/30/2007 7:17 PM, David van der Spoel wrote: Nicolas Sapay wrote: Actually, I have used OpenMosix some time ago in a another life :) All I remember is that NAMD was perfor

[gmx-users] calculation the energy of interaction

Hello everybody, I have a system made of lipid and water and I want to calculate the components of the lipid-lipid, lipid-water and water solvent interactions (LJ+electrostatics). I know there is already a lot of explanations about that kind of stuff on the mailing-list. I have carefully rea

[gmx-users] calculation the force of interaction

tions (LJ+Coulomb). Is it possible to do that in Gromacs without severely hacking the code? I have searched in the mailing-list but have found only few posts about that, all on the developer mailing-list. thanks Nicolas Nicolas Sapay wrote: Hello everybody, I have a system made of lipid and

[gmx-users] Implemetation of the CHARMM27 ff into gromacs : managment of dihedral terms

your answers! Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] about (painful) units conversion

te courses of thermodynamics = 1 kcal = 4.185 kJ Who's right? It's probaly a debat with no end and the three answers are probably correct ;-). But which conversion should be applied in our case? Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 25

Re: [gmx-users] Implemetation of the CHARMM27 ff into gromacs : managment of dihedral terms

ed with 1-4 LJ parameters. Then, it can be possible to define all pair with CT1 with its 1-4 LJ parameters int the pairtypes section and use them to produce the .top... It is probably not a bright solution, but if it can work... Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of

[gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.

s. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.g

[gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters

account in this case? In fact, I have tried to add somd bonds and improper but that generates a chunk of warnings when I use grompp. Sorry for this basic question but I'm still new in Gromacs... Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Scienc

Re: [gmx-users] CHARMM force field implementation in Gromacs :

Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n >= 6 don't come alone. For exemple in Arg : HD1 HE || |// --CG--CD--NE--CZ || \ HD2 is defined by 6 dihedral with n>=6 (C

[gmx-users] CHARMM force field : TIP3 LJ parameters

ral other pairs (with or without CHARMM's 1-4 parameters) : the problem seem to be limited to the OT..HT pair cheers Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869

[gmx-users] Using the CHARMM TIP3P water model in Gromacs

gid water model and then that the H1...H2 distance will be constrained (I don't use the -DFLEXIBLE flag in my .mdp file and use the -I flag ot include the directory where the CHARMM force field is defined). So, is my use of the TIP3P model correct with GROMACS? Thanks for your comments! Nic

[gmx-users] print out energy values with more decimals

Hello, I'm testing an implementation of the CHARMM force field in Gromacs. For the moment, I just work on simple systems and the energies seems to be correct. Gromacs gives energy values with 5 decimals. Is it possible to print these values with 6, 8 or 10 decimals? I want to have a precise idea o

[gmx-users] vdW parameters and atoms moving too fast

simple" and leads to initialiation problems, or if there is some problem of accuracy with non bonded energy when atoms becomes too close and should relax, or I have made a too evident mistake that I cannot fix... Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of

Re: [gmx-users] vdW parameters and atoms moving too fast

A 3.153970e-09 1.292128e-17 [ nonbond_params ] OT HT 1 4.382447e-05 1.371950e-09 [ pairtypes ] OT HT 1 4.382447e-05 1.371950e-09 I have switch off the atom charges after tested tey are not significantly involved in my problem Nicolas > Nicolas SAPAY wrote:

Re: [gmx-users] vdW parameters and atoms moving too fast

> Nicolas SAPAY wrote: >> good remark... here is the files! I precise that modifying the inter-atomic distance doesn't solve the problem and that nb parameters are >> defined in the ffcharm27nb.itp file as follow : >> >> [ atomtypes ] >> OT15.9994

[gmx-users] Urey bradley term in the sum of energies

tween Angle and UB terms? I guess that both parameters are used in the computation but I'm not sure whether they are added before be printed in the .edr file or not. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary A

[gmx-users] How to keep intact hdrogen coordinates from a PDB file

-ignh option but that modified my coordinates... Any suggestion will be welcome! Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311

Re: [gmx-users] How to keep intact hdrogen coordinates from a PDB file

> Nicolas SAPAY wrote: >> Hello everybody, >> >> I want to convert a .pdb file into a .gro using pdb2gmx but I have some >> troubles with hydrogen coordinates : they are all modified by pdb2gmx >> during the process. Actually, all hydrogens have been added previo

[gmx-users] degree of freedom

Hello everybody, I want to know the number of degrees of freedom in my system... Is there a way to calculate that with Gromacs? Nicolas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't p

Re: [gmx-users] degree of freedom

Actually, I had a doubt on what happens when movements of the center of mass are removed and when the position of a molecule is constraint... Just wanted to check my calculations... Nicolas > Nicolas SAPAY wrote: >> Hello everybody, >> >> I want to know the number of deg

Re: [gmx-users] degree of freedom

> Nicolas SAPAY wrote: >> Actually, I had a doubt on what happens when movements of the center of >> mass are removed and when the position of a molecule is constraint... >> Just >> wanted to check my calculations... > > As a suggestion, if you say what your

[gmx-users] How to extend Ryckaert-Bellemans parameters?

structures involved in the R-B potential calculation. Can someone help me? I have already a .itp file with the correct number of parameters. Nicolas ps: I have read the previous posts on the topic... Unfortunately, the parts of the code to modify were not indicated. -- [ Nicolas SAPAY, Ph.D. ] Uni

Re: [gmx-users] How to extend Ryckaert-Bellemans parameters?

David van der Spoel wrote: Nicolas Sapay wrote: Hello everybody, I need to extend Ryckaert-Bellemans parameters to C6 in order to take into account dihedrals in alkyl chains. What parts of the source code need to be modified exactly? I'm sure it is pretty trivial to do that, but I

Re: [gmx-users] How to extend Ryckaert-Bellemans parameters?

Yang Ye wrote: Mark Abraham wrote: Nicolas Sapay wrote: As it is not possible to do that in the ffxxxbon.itp file, I was sure it was the same thing in all other files. But it works perfectly with my .top files... Thanks! /headscratch It should work in the .itp file too, since your .top