[gmx-users] problem with installation of topolbuild1.2.1

Hi Can anybody please tell me how to install topolbuild 1.2.1 programm in  32 bit machine with Fedora linux operating system. I cannot understand the instruction given in the READ ME file Subarna  See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://i

Re: [gmx-users] Fatal error

Hi, Probably you don't have write permissions in that folder. Cheers, Tsjerk On Wed, Jul 8, 2009 at 1:07 AM, s lal badshah wrote: > Hi Gromacs user, > > I changed the version and this time it gave the following error > s...@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o md283-TE.xvg >  

Re: [gmx-users] Convert trr into crd (amber format)

Ragnarok sdf wrote: I came across a tool for making "porcupine" plots out of my PCA analysis, but first I need to perform the analysis with a program that accepts .cdr (amber traj) file format (the name of the program is PCAZIP). I would like to know if there is a way to convert my .trr trajector

[gmx-users] Convert trr into crd (amber format)

I came across a tool for making "porcupine" plots out of my PCA analysis, but first I need to perform the analysis with a program that accepts .cdr (amber traj) file format (the name of the program is PCAZIP). I would like to know if there is a way to convert my .trr trajectories into these .cdr on

Re: [gmx-users] Installation problem:fftw3f lib. not found.

* Shobhit Kudesia [2009-07-08 02:53:22 +0530]: hI, I apologize for late reply. The script you mentioned worked completely fine. I guess I was using different shell. Thanks a lot You're welcome. Just one remark. When setting any CPPFLAGS or LDFLAGS it is often helpful to put this statements i

[gmx-users] Fatal error

Hi Gromacs user, I changed the version and this time it gave the following error s...@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o md283-TE.xvg :-)  G  R  O  M  A  C  S  (-: Gnomes, ROck Monsters And Chili Sauce     :-) 

RE: [gmx-users] Fatal error

The error tells you what the problem is: Fatal error: reading tpx file (em.tpr) version 40 with version 20 program You are trying to read an em.tpr file that was generated using version 40 (as noted by the header it is GROMACS 3.3.1) using a version 20 program (as noted by the header it is

[gmx-users] Fatal error

Hi gromacs users, the other fatal error which is produces from my last year data is: s...@linux-g1cj:~/Desktop/283> g_rms -s em.tpr -f md283.trr -o md283-rmsd.xvg :-)  G  R  O  M  A  C  S  (-:    GROningen MAchine for Chemical Simulation  

[gmx-users] analysis eror

Hi gromacs users. I need help with the old data generated by gromacs. It is about a year older. I used the command and the output is: s...@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o 283te.xvg :-)  G  R  O  M  A  C  S  (-:    Good gRace! Old Maple

Re: [gmx-users] Installation problem:fftw3f lib. not found.

hI, I apologize for late reply. The script you mentioned worked completely fine. I guess I was using different shell. Thanks a lot On Wed, Jul 1, 2009 at 2:11 PM, Florian Dommert < domm...@icp.uni-stuttgart.de> wrote: > * Shobhit Kudesia [2009-06-30 21:19:47 -0400]: > > > Hi, >> >> I installed

Re: [gmx-users] Why is triclinic geometry not retained in confout.gro?

Hi Jenny, Check chapter 3 of the manual regarding PBC. There is no box in PBC (a box defines PBC, but PBC does not define a box). The rectangular brick is just one of the ways to represent the unit cell. If you insist in seeing a triclinic unit cell, use trjconv -ur triclinic -pbc inbox. Cheers,

[gmx-users] Including K+ in gromos96

"Date: Mon, 6 Jul 2009 16:52:51 -0500 From: sadhna joshi Subject: [gmx-users] including K ion in gromos96 To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" hi, I am using gromacs 3.3.1 and ions.itp does not have K ion (in gromos96). I tried to include it

[gmx-users] Why is triclinic geometry not retained in confout.gro?

Hello gmx-users I?m having problems with my mdrun (probably a newbie question). I?m using the latest version of gromacs. I have my .pdb file (or .gro), mdp and .top files ready and can generate the .tpr file. When I run this (with an simple energy minimisation) the simulation runs to com

[gmx-users] using GROMACS in SDS-water simulations

Dear gmx-users, I have a general question: to your knowledge, is there anybody that has used GROMACS previously to simulate a protein in a mixture of SDS+water (not in a micelle or in a layer of SDS)? I searched for papers or publications, but I didn't found anything relevant to my topic. Thanks

[gmx-users] -xy option for g_rdf

Dear GMX-users, I'm using g_rdf -xy for pure water box (about 1000 waters), but it just stopped after selecting two index groups (simply waters). Have you had the same experience with g_rdf -xy?Is it a bug? but, I couldn't find that in the Bugzilla. Any comments will be very appreciated.

[gmx-users] g_energy=> Different Average values from the screen than calculation of .xvg?

Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. EnergyAverage RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034

[gmx-users] Re: g_energy=> Different Average values?

Chih-Ying Lin wrote: Hi I have read through the manual but could not get it. Would you please explain it more? Normally the energy file does not store the value at every step. So the average over all the steps will differ from the average over the stored steps. Mark

Re: [gmx-users] bonds rotating more than 30 and segmentation fault.

you may want to have a look at the cutoff used by the force field you defined your molecule in! 0.5 is definitely too small. did you minimized? if your starting configuration does not correspond to the topology, the use of position restrains (-DPOSRES) if you actually define them will be

Re: [gmx-users] about template.c?

On Tue, 2009-07-07 at 00:35 -0700, Chih-Ying Lin wrote: > Hi > > inside template.c => > > #include "statutil.h" > #include "typedefs.h" > #include "smalloc.h" > #include "vec.h" > #include "copyrite.h" > #include "statutil.h" > #include "tpxio.h" > > what are they? > and, where are they? Those

[gmx-users] bonds rotating more than 30 and segmentation fault.

Dear users, I am trying to simulate a non protein molecule and have included the necessary parameters in the ff*.rtp file. I first encountered an error in the grompp step, so i modified my .mdp files such that the rlist, rvdw and rcoulomb values are set to 0.5. Now, while carrying out the mdrun for

Re: [gmx-users] False C6/C12 parameter for DMSO and chloroform in GROMOS 45a3 force field (ffG45a3)

Hi Roman, checking the mentioned original publication on GROMOS96 finally convinced me that you're right. It even says: "If another combination rule ... is to be used to obtain C6ij and C12ij or if these mixed atom type pair parameters are not related to the single atom type van der Waals pa

Re: [gmx-users] about template.c?

On Jul 7, 2009, at 9:35 AM, Chih-Ying Lin wrote: Hi inside template.c => #include "statutil.h" #include "typedefs.h" #include "smalloc.h" #include "vec.h" #include "copyrite.h" #include "statutil.h" #include "tpxio.h" what are they? and, where are they? Go to the gromacs-4.0.5 directory and

Re: [gmx-users] Where are the source codes?

On Jul 7, 2009, at 9:28 AM, Chih-Ying Lin wrote: Hi I have installed the Gromacs and I want to see the source codes. Which directory can I find them? gromacs-4.0.5/src gromacs-4.0.5/include Carsten ___ gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] xdr library. Just for an example.

Hi Vitali, There should be such code with then library itself. Ran. Vitaly V. Chaban wrote: > Hi, > > Can anybody share any working code which uses xdr-1.1 library? - Just > to consult. > > Thank you very much in advance, > Vitaly ___ gmx-users mailin

[gmx-users] xdr library. Just for an example.

Hi, Can anybody share any working code which uses xdr-1.1 library? - Just to consult. Thank you very much in advance, Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] about template.c?

Hi inside template.c => #include "statutil.h" #include "typedefs.h" #include "smalloc.h" #include "vec.h" #include "copyrite.h" #include "statutil.h" #include "tpxio.h" what are they? and, where are they? thank you Lin /* * $Id: template.c,v 1.4 2001/07/23 15:28:29 lindahl Exp $ * *

[gmx-users] Where are the source codes?

Hi I have installed the Gromacs and I want to see the source codes. Which directory can I find them? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

Re: [gmx-users] using editconf to duplicate membrane

Hi Bing, You do want to use genconf for that (the way you use it, editconf scales the coordinates). genconf -f xxx.pdb -nbox 2 2 1 -o zzz.pdb The thing to make sure is that all molecules are whole before processing them with genconf. The other possibility is to use editconf to translate a few co