[gmx-users]mdrun using old version

help. Nicolas Prudhomme Ph.D. -- 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

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

Hello Anna, If you just need to vizualize the PDB file, you can code the residue Id in hexadecimal and vizualize it with VMD. VMD is able to read hex number in PDB files. Cheers, Nicolas > Hi Anna, > > The 'problem' is the PDB file format. It is a fixed-width format that &

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] 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

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

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

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 >>

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

the bond constraints, but I can't locate precisely where it is. Settle parameters are exactly the same (as well as constraints for flexible water). Did someone ever face a similar problem? Rgards, Nicolas P.S. I My system is just a box of 1728 water molecules pre-equilibrated for 500 ps at

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

of your molecule. None of this tools can generate a Gromacs topology file, however. Regards, Nicolas Tanos C. C. Franca a écrit : Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and

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

manually (from the "representation" menu) to see if it change something. If not, that is probably a bug in the parsing of the gmxdump output. That is where the bonds come from. Cheers, Nicolas After that it gave me the following lines: [ g_cg ] Processing "topol.tpr".

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

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

coordinates: vmd -psf topology.psf -pdb coordinate.pdb You won't see any weird bonds. Nicolas Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.a

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

Hello everybody, Here is the rtf file I mentioned previously. It can be used by PSFGEN to generate a psf file from pdb files. The result can be used, for example, by the PME Electrostatics plugin of VMD. PSFGEN is available as a VMD plugin or as an independant executable. Nicolas Nicolas

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

Hi, All TCL scripts dowloaded from the VMD website as well as mine are supposed to be used within VMD. You have to run VMD first, then source the script. Alternatively, you can source it in your .vmdrc file. After that, you can run the g_cg function Nicolas > > > > >

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

ts history. It doesn't seem too difficult to understand. You should be able to modify it for your own purpose, if needed. Cheers, Nicolas Thomas Schmidt a écrit : Dear Omer, many thanks for your answer, but your solution doesn't work for me. We have Protein-Lipid models in the

Re: [gmx-users] GROMACS to AMBER

size definition. The appropriate output format should be crdbox or boxcrd in VMD. Keep in mind that quite often, converting a trajectory into another format is useless if you don't convert the topology/parameters as well. Regards, Nicolas > Hello all. > > I would like to know if the

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

I remember having a similar issue a long time ago. If I remember correctly, the culprit was a bad parametrization of the Langevin piston. Maybe you should specified how the pressure is controlled, as well as how you managed the center of mass motions in you dynamics. Nicolas > Well the bila

Re: [gmx-users] waters in ion channels

quot;] or set sel [atomselect top "not (water and same resid as (z>20 and z>80))"] then animate write pdb myfile.pdb sel $sel That will select and save in a pdb file all but the water molecules too close to the lipids. Nicolas > > > --- On Fri, 3/7/09, Itamar

Re: [gmx-users] GMX Installation

n also read the documentation available here: http://oldwww.gromacs.org/content/view/23/33/ http://oldwiki.gromacs.org/index.php/Installation Nicolas > Please guide me if you have information on this case. >   >   > Thanks. >   > Mahmoud< > > > __

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

oordinates: animate write pdb sel $sel This is a tidy task and some equilibration is still required after that. Basic knowledge of TCL/VMD scripting languages may be required to facilitate/automate the work. Nicolas Thanks, -Shay -

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

libraries. You also have make sure that you source the appropriate path to mdrun in your script and that your GMXLIB path is correctly set. Hope that helps, Nicolas Payman Pirzadeh a écrit : Hi Justin, Following is the script I use. But remember several points: 1. I compiled the gmx with

Re: [gmx-users] g_covar Segmentation fault

file format conversion. Hope that helps... Nicolas Regards, *Anirban Ghosh* *Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India * Add more friends to your mess

Re: [gmx-users] Problem configuring openMPI

Manik Mayur a écrit : On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <mailto:nsa...@ucalgary.ca>> wrote: Manik Mayur a écrit : Hi, If I have 2 mpi environments, namely LAM and openMPI, and I want gromacs to use openMPI of the two, what extra option

Re: [gmx-users] Problem configuring openMPI

d to use a local installation of openMPI myself, but finally asked my sysadmin to install it for all users. I had many problems with libraries that couldn't be loaded properly. Cheers, Nicolas Thanks, Manik On Tue, Mar 3, 2009 at 10:58 PM, Nicolas <mailto:nsa...@ucalgary.ca>>

Re: [gmx-users] Problem configuring openMPI

se Lam often, though, you might need to use different Lam options. Nicolas Manik Mayur a écrit : Hi, I have till now successfully used openMPI and gromacs together. Recently I got a cluster where I tried to install openMPI and gromacs locally as I donot have root priviledges on it. But i

[gmx-users] buffer reading error with grompp

stallation using the following commands: include=$HOME/local/bin/fftw-3.2.1/include library=$HOME/local/bin/fftw-3.2.1/lib ./configure --prefix $HOME/local/bin/gromacs4-test --without-x CC=/usr/bin/gcc CPPFLAGS=-I$include LDFLAGS=-L$library Thanks, Nicolas begin:vcard fn:Nicolas S

Re: [gmx-users] g_wham Error bars

rough estimate of the error. Hope that helps, Nicolas Raphael Alhadeff a écrit : Hello everyone, I wanted to ask if anyone knows how to compute standard deviation, for the sake of adding error bars to an energy profile output using g_wham (PMF using umbrella sampling in my case). Just to cl

Re: [gmx-users] P-N vector orientation

ked to calculate the NP dipole orientation. I've done that one time, but it was only for a particular lipid in a membrane, not for the whole bilayer. IIRW, the result was the same than the one of my scripts and the calculation was much faster. Nicolas ANINDITA GAYEN a écrit : Dear Xav

Re: [gmx-users] P-N vector orientation

Hello, Is that thread solved? I've got a bunch of TCL scripts for VMD that can do this calculation. They are not really user friendly or incredibly fast, but they give a correct answer. I can send those scripts off the list if you are interested. Nicolas ANINDITA GAYEN a écrit :

Re: [gmx-users] Best performace with 0 core for PME calcuation

Carsten Kutzner a écrit : On Jan 10, 2009, at 8:32 PM, Nicolas wrote: Berk Hess a écrit : Hi, Setting -npme 2 is ridicolous. mdrun estimates the number of PME nodes by itself when you do not specify -npme. In most cases you need 1/3 or 1/4 of the nodes doing pme. The default -npme guess of

Re: [gmx-users] Best performace with 0 core for PME calcuation

Mark Abraham a écrit : Nicolas wrote: Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system is 9.

Re: [gmx-users] Best performace with 0 core for PME calcuation

cores. So, setting npme to 0 systematically gives the best results. I have also tested -1. With, npme set to -1, the performances are the same than for 0 until 8 cores. Above that, the guess is not so efficient. Nicolas Berk > Date: Fri, 9 Jan 2009 18:37:37 -0700 > From: nsa...@ucalg

Re: [gmx-users] Best performace with 0 core for PME calcuation

Nicolas a écrit : Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system is 9.6x9.6x10.1 nm^3. I&#

[gmx-users] Best performace with 0 core for PME calcuation

tion for that? Does that means domain decomposition is useless below a certain real space cutoff? I'm quite confused. Thanks, Nicolas begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;

[gmx-users] About the -npme option of mdrun and domain decomposition

PME), will I limit the loss of efficiency anyway (even by few percent)? Thanks Nicolas begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:nsa...@ucalgary.ca title:Post-doctoral fello

Re: [gmx-users] DNA will not stay in the middle of the box

, removing the COM motions of only one component of your system is very probably a bad idea. You should rather use position restraints. If you look in the mailing-list or the manual, you will quickly find how to do that. Regards, Nicolas For the old version (3.3.2) it worked but now (4.0.2) there are

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

onvenient to write a Python or a Perl script to do this kind of stuff, though. Nicolas Regards, Suman. ___ 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] Analyzing a trajectory split over multiple files

pendent. For a long time scale phenomenon, you will have to split your trajecory in bigger pieces or even merge all the parts. Please help. Regards, Suman. begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;

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

t. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[

Re: [gmx-users] gromacs 3.3.1/4.0 and fftw 3.1.2

luster Y) and didn't notice any significant difference, but as I said, it was a quick comparison. Additionally, it is said on the website that Gromacs is compatible with fftw-3.x: http://www.gromacs.org/content/view/23/33/ Nicolas Thanks, Chris. __

Re: [gmx-users] a question about template.c

nd it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PR

[gmx-users] g_hbond, residue selection and boundary conditions

Thanks in advance for you answer, Nicolas begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:Research Assistant tel;work:403-220-6869 x-mozilla-html:TRUE url:htt

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] 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 2

Re: [gmx-users] Leaflet of Bilayer

the number of PC in the upper leaflet, assuming 1) the phosphorus atom is named P8 and 2) the bilayer is center on 0.0 along the z axis. Nicolas 2.Is there anyway to increase popc and water numbers by mentioning specific molecules number? Not that I'm aware of. There is a -maxsol op

Re: [gmx-users] still system exploid

. Nicolas About mdp that has a popc, I should say that this mdp was fpr my membrane which i used it before and i just change some of the parameter of this file and because the name was not important i did not change it. I am sorry my gro file is big and because of this the gmxmail servic avoid to

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] 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: 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

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

processors, Red Hat 4.5, gcc/mpicc 3.4.6. Thanks a lot for your advices -Nicolas begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:PhD tel;work:(403) 220-6869 t

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

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

x27; in Coul-SR:SOL-SOL mean? It's in g_energy when it asks to select terms for analysis. JAL> SR = short-range begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAI

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

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] 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

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

st but I still obtain the same error with the rb1 test (and the dec+water test). Can someone explain to me what the it means exactly and how to fix it? (I guess it's related to the Ryckaert-Bellemans potential?). Thanks, Nicolas ps: I'm using RHE 4.7 and gcc 3.4.6 begin:vca

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] <mailto:[EMAIL PROTECTED]>> wrote: We also have a implementation of CHARMM(27) for Gromacs, but without CMAP as w

Re: [gmx-users] CHARMM FF

particular to difficulty to makes the water loop working for CHARMM TIP3P... Is it planed to implement that into the CVS version? Nicolas Roland Schulz a écrit : Hi all, who has the CHARMM FF working with Gromacs? I heard that Erik's group has something working. Is this correct? My impressi

Re: [gmx-users] CHARMM to Gromacs

] Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:Ph

[gmx-users] Question about different versions of gromacs

this? Thanks in advance Nicolas Martinez ___ 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 before posting! Please don't post (un)subscribe req

[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] calculation the energy of interaction

read all the answers... A tutorial about that would be great! Thanks in advance for your comments Nicolas begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED

[gmx-users] nstlist with vdw only

Would't this mean, that molecules could suddenly appear and lead to a discontinuity in the LJ-potential? Or in what way should I modify the r_vdw according to what rlist? I wanna end with a cut-off of the LJ-potentail around 1.75nm. Thanks in advance Nicolas Erik Lindahl wrote: Hi Nic

[gmx-users] nstlist with vdw only

Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation

Re: [gmx-users] how to build up fixed connections? how to simulate no electrostatics?

ssure regulation? (If so, with which barostat?) (b) How do you know what you expect the pressure to be? (c) By "fixed connections", do you mean fixed bond lengths? Are you doing this using constraints? David On 8/13/07, Nicolas Schmidt <[EMAIL PROTECTED]> wrote: Hey everybody.

[gmx-users] how to build up fixed connections? how to simulate no electrostatics?

ation runs fine I'm unhappy with the results, cause pressure is higher than I expect it to be. Since Mark told me, I'm not simulating fixed connections I'd like to ask if ANYBODY could help me with that. Thanks in advance Nicolas -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adresse

[gmx-users] Re: doing simplest simulations

s amount of molecules) to compare gromacs' speed in simulating large systems of simple gas molecules. I wanna do well, otherwise I'd just take what I got from the already finished simulations. But afterwards I'm done and won't bother you again. ;-) Thanks again. Nicolas po

Re: [gmx-users] doing simplest simulations

ar), of course I'm only measuring at the end of my siimulation run. Changed the thermostat and r_list, so maybe that was the problem. Thanks anyway and in advance Nicolas Mark wrote: Nicolas Schmidt wrote: Hi, I'm doing a comparison in the aspect of speed between gromacs and an other MD-s

[gmx-users] doing simplest simulations

;m asking you to take a look at my files (added all necessary ones) and correct me (they are less big than you might emagine, resulting from the pretty simple molecules I'm buidling up) Thanks in advance Nicolas ___ gmx-users ma

[gmx-users] add to "doing simplest simulations

Sorry 'bout that, this time with the files... Gromacs Runs One Microsecond At Cannonball Speeds 2 1ETHET11 0.769 0.769 0.744 1ETHET22 0.769 0.769 0.794 1.53748 1.53748 1.53748 #include "ffgmx.itp" #include "OneEthane.itp" [ system ] ;Name pure etha

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

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

[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

[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] seriell but parallel ???

Dear gromacs-users, First of all thanks to all contributers of the answers considering my first issue, actually this was my first simulation on gromacs, so maybe this explains my kind of unnecessary questions ;-) Anyway, again a probably easy to solve problem: I only got the possibility to ru

[gmx-users] bondtype 5

This may be a really simple question, I know, but still... How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards): WARNING 1 [file "e

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

Sorry, the message has been sent too fast, the 4 bonds have been correctly created now. So, the correct specbond line is: CYS SG 1 ZN2 ZN 1 0.25 CYSZZN There is still an angles that lacks (the S-ZN-S angle), but I can add it manually. Nicolas Sorry for

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

[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] 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

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

[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] 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

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

[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&#

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] 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] MD of crystal

My apologies. Magically things did work now :) nick On Fri, 2007-02-16 at 16:07 +0100, David van der Spoel wrote: > Nicolas Bock wrote: > > I named it conf.gro since genconf seemed to like that name. Where in the > > gromacs manual does it describe the format of a gromos

Re: [gmx-users] MD of crystal

I named it conf.gro since genconf seemed to like that name. Where in the gromacs manual does it describe the format of a gromos96 file? I only found references to the gromos96 manual but I couldn't find a file format description in the online version of it either. Could you point me to the right pl

Re: [gmx-users] MD of crystal

; time to get it started but you can do it. > > /Calle > > Nicolas Bock wrote: > > Hello list, > > > > I would like to run an MD simulation to simulate the melting of a > > metallic crystal. Can this be relatively simply done in GROMACS? I > > have t

[gmx-users] MD of crystal

Hello list, I would like to run an MD simulation to simulate the melting of a metallic crystal. Can this be relatively simply done in GROMACS? I have the pair potential between the ions and ion configurations I would like to start with. I tried to work my way through the GROMACS manual but I am ha

[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

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

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:

[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] mixing rules for LJ parameters?

Mixing rules only apply when no specific parameters for an interaction are provided. "Gromacs FF" is mostly GROMOS87 (i.e., don't use it for new runs), which has a handful of exceptions from the standard combination rules. What do you mean by "new runs"? And why not use it? Parameters are to

[gmx-users] mixing rules for LJ parameters?

Hi, I'm trying to understand how the LJ parameters are determined in the Gromacs FF, namely the file ffgmxnb.itp. According to the mixing rules given on page 88 of the manual c6 and c12 for interactions between atoms should just be the square root of the product of the individual atom paramete

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

idea of the accuracy of this implementation. Additionaly, can someone confirm that the electrostatic-to-energy conversion factor is indeed 138.935485 kJ.nm/mol.e by default? Thanks Nicolas ___ gmx-users mailing listgmx-users@gromacs.org

[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

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