Re: [gmx-users] rdf

Hi, 100 ns is overkill for those liquids. It should be smooth enough at 1 ns, provided you average g(r) over every molecule. What do you mean the volume decreases? With time? As for the cut-off, it's well known that switching Coulomb terms leads to artifacts, and increasing the cut-off distanc

[gmx-users] rdf

Hi, I am doing rdf's of simple molecules. I ran my simulation of water and methane for 100ns to get a smoother curve for the rdf. I am trying to determine the volume, and after a certain cut-off I would assume my values to be constant (i.e. volume), but the values fluctuate alot (i.e. d

Re: [gmx-users] xtc error

On 1/30/10 8:29 PM, neo lotus wrote: Hi ,I am running to program, suddenly in the 200 steps .program Pull In .( in .mdp file dt was 0.002 and nsteps was 400) and I see following error : { xtc error –maybe you are out of quota }.please guide me .thanks. Sounds like your file hit

[gmx-users] xtc error

Hi ,I am running to program, suddenly in the 200 steps .program Pull In .( in .mdp file dt was 0.002 and nsteps was 400) and I see following error : { xtc error –maybe you are out of quota }.please guide me .thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

I am using openmpi-1.4.1. -- Chandan kumar Choudhury NCL, Pune INDIA On Sun, Jan 31, 2010 at 12:34 AM, Chandan Choudhury wrote: > Hi Ronald !! > Thanks for your reply. > I recompiled the openmpi. But while executing ./configure --enable-mpi in > gromacs4.0.7 the following error is shown in con

Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

Hi Ronald !! Thanks for your reply. I recompiled the openmpi. But while executing ./configure --enable-mpi in gromacs4.0.7 the following error is shown in config.log file. configure:4536: checking for mpicc configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc configure:4563: result: mpicc conf

Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

Hi, your MPI installation has to be brogen. mpicc always has to be able to find libmpi. Please reinstall mpi correctly. Roland On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury wrote: > Hi gmx users !! > > On compiling GMX paralley, following error was encountered. How can I > tackle this. >

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

bharat gupta wrote: thanks for the advice sir .. Actually I have to study how the interaction between a coiled peptide and a protein takes place through simulation .. and i am new to simulation .. i know a little theory about simulation .. so can u suggest me how to start ... and will it poss

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

thanks for the advice sir .. Actually I have to study how the interaction between a coiled peptide and a protein takes place through simulation .. and i am new to simulation .. i know a little theory about simulation .. so can u suggest me how to start ... and will it possible to complete my work

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

bharat gupta wrote: here is the link for that tutorial ... What link? and one more thing I wanna ask that in the tutorial he has asked to download to .mdp file (like ions.mdp) . My doubt is .. I should know the theory for creating such files for the system of my study .. That's what the

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

here is the link for that tutorial ... and one more thing I wanna ask that in the tutorial he has asked to download to .mdp file (like ions.mdp) . My doubt is .. I should know the theory for creating such files for the system of my study .. Bharat -- gmx-users mailing listgmx-users@gromacs

[gmx-users] error: Cannot compile and link MPI code with mpicc

Hi gmx users !! On compiling GMX paralley, following error was encountered. How can I tackle this. Kindly help. checking for mpicc... mpicc checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc The config.log file reads configure:4536: check

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

Hi Bharat, Besides the notes of Justin, which lysozyme tutorial? And for which GMX version was that tutorial written? Tsjerk On Sat, Jan 30, 2010 at 12:53 PM, Justin A. Lemkul wrote: > > > bharat gupta wrote: >> >> Hi >> >> I am getting the follwing error while running the mdrun command given >

Re: [gmx-users] problem with position restraints: X0 set to zero

Julian Garrec wrote: Dear GROMACS users, I am trying to equilibrate my system (monomeric protein in water) and I want to use position restraint on heavy atoms of the solute using the posre.itp file. For some reason, grompp applies correctly the force constant I want, but sets all the refere

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

bharat gupta wrote: Hi I am getting the follwing error while running the mdrun command given in the step six of the lysozyme tutorial :- Program mdrun, VERSION 4.0.7 Source code file: gmxfio.c, line: 737 Can not open file: topol.tpr --- "

Re: [gmx-users] Fwd: xmgrace

On Sat, 2010-01-30 at 12:03 +0100, David van der Spoel wrote: > On 1/30/10 11:04 AM, bharat gupta wrote: > > Sir > > > > I am installing openMotif-2.2.3 version but after make command I > > getting the follwoing error :- > > > Why not use the redhat software: > > yum install openmotif-devel > > o

Re: [gmx-users] Fwd: xmgrace

On 1/30/10 11:04 AM, bharat gupta wrote: Sir I am installing openMotif-2.2.3 version but after make command I getting the follwoing error :- In file included from XmStrDefs.c:10: ../Xm/Xm.h:59:34: error: X11/extensions/Print.h: No such file or directory In file included from XmStrDefs.c:10: ../

[gmx-users] cavity point

Hi all, I have done the normal mode analysis of pbp5 protein.Now I am looking the cavity points in this protein. There are 47 cavity points in this protein. Now is there any way to find the relationship between cavity points and the active site of the protein by analyzing the normal modes

[gmx-users] Re: Step 6 of lysozyme tutorial

Hi I am getting the follwing error while running the mdrun command given in the step six of the lysozyme tutorial :- Program mdrun, VERSION 4.0.7 Source code file: gmxfio.c, line: 737 Can not open file: topol.tpr --- "This Doesn't Suck, It's

[gmx-users] Re: GRACE

Hi all Can anybody tell me which version of GRACE shall i install for red hat linux 5 since i am getting errors after compilation ?? -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx

Re: [gmx-users] Fwd: xmgrace

Sir I am installing openMotif-2.2.3 version but after make command I getting the follwoing error :- In file included from XmStrDefs.c:10: ../Xm/Xm.h:59:34: error: X11/extensions/Print.h: No such file or directory In file included from XmStrDefs.c:10: ../Xm/Xm.h:827: error: expected specifier-qual

[gmx-users] problem with position restraints: X0 set to zero

Dear GROMACS users, I am trying to equilibrate my system (monomeric protein in water) and I want to use position restraint on heavy atoms of the solute using the posre.itp file. For some reason, grompp applies correctly the force constant I want, but sets all the reference positions to zero. O

Re: [gmx-users] Fwd: xmgrace

On 1/30/10 10:30 AM, bharat gupta wrote: hi all, I am trying to install xmgrace on redhat linux 5 and I am getting the following two errors after running the ./configure command :- checking for a Motif>= 1002 compatible API... no configure: error: M*tif has not been found Can u pls tell how c

[gmx-users] Fwd: xmgrace

hi all, I am trying to install xmgrace on redhat linux 5 and I am getting the following two errors after running the ./configure command :- checking for a Motif >= 1002 compatible API... no configure: error: M*tif has not been found Can u pls tell how can I rectify the error .. or shall I go fo