Re: [gmx-users] atomnumber=-12345

Itamar Kass wrote: Hi Dallas, Thank for the replay. I think that I found what was "wronge". I have created the tpr files using GROMACS 3.3.3 but used gmxdump (-sys) from the GROMACS 4.0.5 package, not a very smart thing to do, ha? I guess this was the source of my error. The .tpr file fo

Re: [gmx-users] atomnumber=-12345

Hi Dallas, Thank for the replay. I think that I found what was "wronge". I have created the tpr files using GROMACS 3.3.3 but used gmxdump (-sys) from the GROMACS 4.0.5 package, not a very smart thing to do, ha? I guess this was the source of my error. Thanks, Itamar On 21/01/10 1:36 PM,

RE: [gmx-users] atomnumber=-12345

Might be a good idea to provide the input and output that generated the error. 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.au +61 3 9903 91

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

Justin A. Lemkul wrote: Krzysztof Mlynarczyk wrote: Hello, On Peter Tieleman's website we can find topologies for various popular lipids. However those seem to be valid for the deprecated GROMOS87 force field. The g96_lipids.itp file is still unavailable. I'd like to run a simulation of

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

Krzysztof Mlynarczyk wrote: Hello, On Peter Tieleman's website we can find topologies for various popular lipids. However those seem to be valid for the deprecated GROMOS87 force field. The g96_lipids.itp file is still unavailable. I'd like to run a simulation of 7TM protein embedded into P

[gmx-users] Lipid parameters for GROMOS96 force fields

Hello, On Peter Tieleman's website we can find topologies for various popular lipids. However those seem to be valid for the deprecated GROMOS87 force field. The g96_lipids.itp file is still unavailable. I'd like to run a simulation of 7TM protein embedded into POPC membrane. G43a2x seems to be a

[gmx-users] atomnumber=-12345

Hi, After one of my simulation had crashed, I had used gmxdump to look into it. What stoke me was the all atoms have the same atomnumer: atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01, q= 1.29000e-01, mB= 1.40067e+01, qB= 1.29000e-01, resnr=0, atomnumber=-12345} at

Re: [gmx-users] How to insput more than two PDB files to use for MD run

pawan raghav wrote: Dear, Is it possible to compare more than two pdb files MD simulations in a single run? how? I don't understand what you're asking. Do you want to compare MD simulations? Run MD simulations with multiple structures? Please clarify and provide specifics of what you

[gmx-users] How to insput more than two PDB files to use for MD run

Dear, Is it possible to compare more than two pdb files MD simulations in a single run? how? -- Pawan -- 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! Please don't po

Re: [gmx-users] Fw: Re: Polymer-protein problem

P.R.Anand Narayanan wrote: - Forwarded Message *From:* P.R.Anand Narayanan *To:* gromacs *Sent:* Mon, 18 January, 2010 12:12:45 PM *Subject:* Re:Re: Polymer-protein Dear Gromacs users, I have to attach a chemical polymer to a protein and when I created peptide bonds and saved it

[gmx-users] Fw: Re: Polymer-protein problem

- Forwarded Message From: P.R.Anand Narayanan To: gromacs Sent: Mon, 18 January, 2010 12:12:45 PM Subject: Re:Re: Polymer-protein Dear Gromacs users, I have to attach a chemical polymer to a protein and when I created peptide bonds and saved it, the entire format of the pdb file c

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

On 01/21/10, Jiang Shin-Lin wrote:Hi, all!I try to install mdrun_mpi today and I got some error.checking for mpxlc... nochecking for mpicc... mpiccchecking whether the MPI cc command works... configure: error: Cannot compile and linkMPI code with mpiccAbove is the error message.As the con

Re: [gmx-users] how to analysis crystal structure and 2D projections by PCA?

Xi Zhao, Find some elementary text on PCA and read it thoroughly. Tsjerk On Wed, Jan 20, 2010 at 2:40 PM, xi zhao wrote: > > Dear users: > I want to analyse a crystal structure by PCA, and want to show its 2D > projection, but I meet errors" segment fault" > my procedure: > g_covar_d -f crysta

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

Hi, all! I try to install mdrun_mpi today and I got some error. checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc Above is the error message. I asked the net manager install ope

[gmx-users] how to analysis crystal structure and 2D projections by PCA?

Dear users: I want to analyse a crystal structure by PCA, and want to show its 2D projection, but I meet errors" segment fault" my procedure: g_covar_d -f crystal strucutre.pdb -s crystal strucutre.pdb  -o eig.xvg -v eig.trr g_anaeig_d -f  crystal strucutre.pdb -eig eig.xvg -v eig.trr -2d 2d.

[gmx-users] problem with vsite and particle decomposition

Great! Thanks. Serena > Hi, > > I fixed the bug for 4.0.8 (if it will ever be released). > > You can work around it by put your protein in a big box and using long > cut-off's > with domain decomposition (or simple run in serial). > > The next version of Gromacs will support domain decompos

RE: [gmx-users] problem with vsite and particle decomposition

Hi, I fixed the bug for 4.0.8 (if it will ever be released). You can work around it by put your protein in a big box and using long cut-off's with domain decomposition (or simple run in serial). The next version of Gromacs will support domain decomposition also for vacuum simulations, even with

[gmx-users] problem with vsite and particle decomposition

Hi, yes, I've just filed a bugzilla and attached the tpr. Thanks, Serena > Hi, > > This is clearly a bug. > Could you file a bugzilla and attach the tpr file? > > Thanks, > > Berk >/ Date: Wed, 20 Jan 2010 08:52:27 +0100 />/ From: sdonnin at gwdg.de

RE: [gmx-users] problem with vsite and particle decomposition

Hi, This is clearly a bug. Could you file a bugzilla and attach the tpr file? Thanks, Berk > Date: Wed, 20 Jan 2010 08:52:27 +0100 > From: sdon...@gwdg.de > To: gmx-users@gromacs.org > Subject: [gmx-users] problem with vsite and particle decomposition > > Hallo, > > I had a problem when runn