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: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hi Nehme, I've did simulations on TRAIL, which also contains a zinc-finger domain, involving three cysteines and a chloride ion. But it's not so simple. Luckily the exact parameters seemed not that vital, as the zinc apparently functions to keep the three subunits together and was in any case not

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

Hi, On Tue, 19 May 2009 14:23:07 -0600, Payman Pirzadeh wrote > Hi Justin, > Following is the script I use. But remember several points: > ${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path > ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest You have a dot before /global/...

[gmx-users] Failing installation with --enable-mpi option

I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix="_mpi" it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix="_mpi" checking build system type...

Re: [gmx-users] Failing installation with --enable-mpi option

Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix="_mpi" it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix="_mpi" checking buil

Re: [gmx-users] Failing installation with --enable-mpi option

Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul : > > > Bhanu wrote: >> >> I tried to install Gromacs on my Core2Quad pc with the command >> >>  ./configure --enable-mpi --disable-nice --program-suffix="_mpi" >> >> it is showing the following error result: >> >> [sand...@bhanu

[gmx-users] autocorrelation functions from several simulations d

Hi all, I have some doubts regarding the general use of acfs. The molecule I am studying is formed by two polycyclic aromatic sub-units joined by a 20-alkene "chain"; it is something like this: /--\/--\ /--\/--\ A | | |-CH2-CH-CH2-CH-CH2(...)| | | B \--/\--/

[gmx-users] Dihedral definition

Dear all, i have a simple question regarding definition of proper & improper dihedral type in gromacs. As in ffgmxbon.itp. [ dihedraltypes ]   ; j    k func  phi0  cp   mult     C   OA    1   180.000  16.736   

[gmx-users] Help with nitrile group in complx protein-ligand md

Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of nu

Re: [gmx-users] Help with nitrile group in complx protein-ligand md

Jocley Araujo wrote: Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the

Re: [gmx-users] Help with nitrile group in complx protein-ligand md

Jocley Araujo wrote: Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied th

[gmx-users] pdb2gmx file error

Hi Justin I am trying to prep a pdb file for md but keep on getting this error message Fatal error: Chain identifier 'O' was used in two non-sequential blocks (residue 2400, atom 18726) Fatal error: But when I look at the file I only have one chain identifier. Also when I strip off hydrogens an

Re: [gmx-users] g_clustsize method

It would be very advantageous for me to have a g_clustsize that could implement the Jarvis-Patrick method instead of single linkage. Would this be very difficult to achieve? Or would it be easy enough to use source code from g_cluster and do a sort of transplant? Thank you for you help >>> David

Re: [gmx-users] Dihedral definition

ANINDITA GAYEN wrote: Dear all, i have a simple question regarding definition of proper & improper dihedral type in gromacs. As in ffgmxbon.itp please upgrade your force field. For most force fields there is a proper description but there is not for this one. Therefore we

[gmx-users] Re: pdb2gmx file error

Please keep all Gromacs-related correspondence on the gmx-users list; I do not advertise as a free tutor :) yimnai forlemu wrote: Hi Justin I am trying to prep a pdb file for md but keep on getting this error message Fatal error: Chain identifier 'O' was used in two non-sequential blocks (re

Re: [gmx-users] g_clustsize method

Jacob Spooner wrote: It would be very advantageous for me to have a g_clustsize that could implement the Jarvis-Patrick method instead of single linkage. Would this be very difficult to achieve? Or would it be easy enough to use source code from g_cluster and do a sort of transplant? Thank you

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

Hi Nicolas, Thanks for the tips! Yes, that's what I thought yesterday. Main problem is I think there is an older version of GROMACS installed on Glacier and if I do not source the path, it will take the cluster one not mine. I passed that phase. Now I am checking if I can run the job in parallel wi

[gmx-users] Lipids forming unsual bonds

Hi ALL, I am simulating a GPCR protein in a POPC bilayer. I have followed Justins' tutorial to set up the system, but have used POPC instead of DPPC. I have used the same parameters given in that tutorial. Till equilibration everything went well. But after releasing the protein in the productio

RE: [gmx-users] Lipids forming unsual bonds

What exactly do you mean by "unusual cross bonds"? I suspect what you are seeing is simply a visualisation artifact, with a molecule being displayed across a PBC in the viewer you are using. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceut

Re: [gmx-users] Lipids forming unsual bonds

Anirban Ghosh wrote: Hi ALL, I am simulating a GPCR protein in a POPC bilayer. I have followed Justins' tutorial to set up the system, but have used POPC instead of DPPC. I have used the same parameters given in that tutorial. Till equilibration everything went well. But after releasing the p

[gmx-users] Lipids forming unsual bonds

"the lipids are forming usual cross bonds (seen in the form of long straight lines)" lines? on what? You need to do a much better job of describing your problem and your observations before anyone can give you a better suggestion than "remove those lines and everything will be solved"...

Re: [gmx-users] Failing installation with --enable-mpi option

Dear Justin, could you please write what environmental changes you made to MPICC.. I tried to alter the profile, but it is rejecting all of them.. Bhanu. On 20/05/2009, Bhanu wrote: > Thanks Justin, will try your suggestion.. > > 2009/5/20 Justin A. Lemkul : > > > > > > Bhanu wrote: > >> > >> I