[gmx-users] simulation in the high temperature

Dear Justin I want to simulate a protein in the high temperature (338 K). I wan to know changing of ref_t in mdp file is enough and there is not any other parameter to be changed in this regard? and how much the results of this type of simulation (in high temperature) is reliable? thanks in advance

Re: [gmx-users] g_covar & g_anaeig problems

Hey, taking fewer atoms by ignoring the hydrogens is a good advice. Thanks a lot. I was wondering if a more appropriate error message could be generated before the program messes around in the memory. The program acts as if it could handle the system size and then crashes with a Segmentation

[gmx-users] Generalized Born segfaults with v4.5.1

Dear friends, when trying to run a double precision vanilla MD, version 4.5.1, with a small hairpin molecule (248 atoms) in implicit solvent (generalized Born approximation) this is what I get: - Getting

Re: [gmx-users] Generalized Born segfaults with v4.5.1

Hi! I am currently working on another issue with the GB-double precision loops. I'll include this as well. But your pdb-file only contains 1 residue with the name UNK (by openBabel). Could you please send me another pdb-file that reproduces this error off-list, and I'll get to it. Cheers /Per

Re: [gmx-users] Generalized Born segfaults with v4.5.1

Hi, I had sent a wrong PDB file, right one sent offlist. Cheers Silvio Il Tuesday 07 September 2010 10:06:15 Per Larsson ha scritto: > Hi! > > I am currently working on another issue with the GB-double precision loops. > I'll include this as well. > But your pdb-file only contains 1 residue w

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Hi, > One work-around for the -chainsep situation you've observed is to remove or > rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when > it tries to merge the chains. It should be taking care of that itself, but > handling it yourself might help. pdb2gmx can probably

[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

I want to restrain certain atoms of my simulation to the plane perpendicular to the bilayer normal, and at the bilayer center. Can someone please provide a quick guide on how to do this? I read the pull-code options, but restraining to a plane did not seem possible? -- Maria G. Technical Univer

[gmx-users] git gromacs

Hi there, Now that gromacs 4.5.1 is released I was wondering which branch should I checkout if I want to test the bleeding edge gromacs development. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Roa

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Dear Gromacs Users, thanks for all your suggestions. Tsjerk, I did try your idea, but unfortunately doesn't seem to work. the pdb file is shared here : http://www.4shared.com/account/file/ijofD83b/DIMER.html newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh Fatal error: Atom OXT in residu

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Hi Nahren, Can you paste your actual command line where you used sed? Cheers, Tsjerk On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel wrote: > Dear Gromacs Users, > > thanks for all your suggestions. > > Tsjerk, I did try your idea, but unfortunately doesn't seem to work. > > the pdb file is sh

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Dear Gromacs Users, Tsjerk, the original file did not contain OXT, as you can see, it has O1 & O2, so I removed the O2 from the PDB and renamed O1 to OXT. ATOM   2841  HG  CYS R 283 -24.270  89.566  -4.957  1.00  0.00   H ATOM   2842  C   CYS R 283 -25.867  92.922  -7.562  1.00 

[gmx-users] membrane protein-free energy

Hi, I have done MD simulations of membrane-protein. I want to calculate interaction energies between protein and headgroup, protein and hydrophobic core (in the bilayer). Please can anyone suggest me the method that should be followed to carry out these analysis. kind regards and best wishes,

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

shiva birgani wrote: Dear Justin I want to simulate a protein in the high temperature (338 K). I wan to know changing of ref_t in mdp file is enough and there is not any other parameter to be changed in this regard? If you need to generate velocities, then gen_temp should also be set to this

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

maria goranovic wrote: I want to restrain certain atoms of my simulation to the plane perpendicular to the bilayer normal, and at the bilayer center. Can someone please provide a quick guide on how to do this? I read the pull-code options, but restraining to a plane did not seem possible?

Re: [gmx-users] membrane protein-free energy

Poojari, Chetan wrote: Hi, I have done MD simulations of membrane-protein. I want to calculate interaction energies between protein and headgroup, protein and hydrophobic core (in the bilayer). Please can anyone suggest me the method that should be followed to carry out these analysis. Plea

Re: [gmx-users] git gromacs

Hi Alan, 'bleeding edge' gromacs development is as always in the 'master' branch. The latest bugfixes for the 4.5.x versions you are going to find in the 'release-4-5-patches' branch. Carsten On Sep 7, 2010, at 12:09 PM, Alan wrote: > Hi there, > > Now that gromacs 4.5.1 is released I was won

Re: [gmx-users] git gromacs

Thanks Carsten. I am trying release-4-5-patches and now I can see it's compiling and installing. However, 'make install' puts the bins only in /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links' or similar to have the gmx bins in /usr/local/bin. I am using cmake. Thanks,

[gmx-users] Restarts: Truncation of file *.xtc failed

Dear Gromacs users I am experiencing a problem with restarts in a REMD simulation with explicit solvent in Gromacs 4.0.5. I am trying to continue a set of simulations that finished after the maximum time in our cluster queue had been reached. Therefore I just directly (i.e. without modifying my inp

Re: [gmx-users] git gromacs

On 9/7/10 1:19 PM, Alan wrote: I am trying release-4-5-patches and now I can see it's compiling and installing. However, 'make install' puts the bins only in /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links' or similar to have the gmx bins in /usr/local/bin. I am us

Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

The manual does discuss restraining to a plane, but this must be the plane in which the atom is already present. [ position_restraints ] ; ai functfc ... 3 1 1000 0 0 How about restraining the atom to some other plane? For example, how about restraining a phosphate group initially

Re: [gmx-users] git gromacs

If using links or simply copying in /usr/local/bin I don't mind, but it would easier, at least for me, once installing gromacs from source to be able to have the gmx bins in /usr/local/bin and, of course, be able to uninstall all gromacs as well (and undoing links or removing copies from /usr/local

[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

Maria, try this. There actually is a lot of this on the mailing list, so I suggest checking it a little deeper for your next querry, or at least outlining how you looked and what you found so that it is clear you have tried. Also, read about pull_pbcatomN and think carefully about how you w

Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

This has been fixed with Berk's commit c06ee471... The error was not related to GB, but rather a combination of domain decomp.+nm+cut-offs. Cheers /Per 6 sep 2010 kl. 11.38 skrev Ehud Schreiber: > Dear GROMACS users, > > I am encountering a couple of issues when trying to perform normal mode

RE: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

Hi, For the moment you can add the option -nt 1 to mdrun, which will make it run without problems. Berk From: per.lars...@sbc.su.se Subject: Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis Date: Tue, 7 Sep 2010 16:12:28 +0200 To: gmx-users@gromacs.org This h

[gmx-users] Re: gmx-users Digest, Vol 77, Issue 33

Hello Justin, 1- Actually since I was focusing on rdf for C-C I didnt explain my understanding from that post well. Anyway, I have only C and H in the system and no protein. You mean I have to make separate groups of C and H for all polymer chains by hand? I trying to find a more smart way of doin

Re: [gmx-users] about rdf

Moeed wrote: Hello Justin, 1- Actually since I was focusing on rdf for C-C I didnt explain my understanding from that post well. Anyway, I have only C and H in the system and no protein. You mean I have to make separate groups of C and H for all polymer chains by hand? I trying to find a m

[gmx-users] gmx 4.5.1 and opemm not compiling on Mac SL

Hi there, I am trying: ~/Downloads/gromacs-4.5.1/build% cmake -DGMX_OPENMM=ON .. ~/Downloads/gromacs-4.5.1/build% make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/

Re: [gmx-users] Restarts: Truncation of file *.xtc failed

Hi, How big is your file? I assume since you are running 18ps simulation, it might be big. I remember there's a problem with gromacs not being able to truncate file size >4Gb. Greg On Tue, Sep 7, 2010 at 8:04 AM, David de Sancho wrote: > Dear Gromacs users > I am experiencing a problem with

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Hey Nahren, > > sed -i '/^ATOM.*O2/d' DIMER.pdb > > Am i going wrong here? You should try :) But it looks quite okay to me ;) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / Un

[gmx-users] hessian.mtx----> readable format

Dear Gromacs Users, Is there a way to convert the hessian.mtx file into a readable format using any of the gromacs utilities? Any help on this would be highly apprecaited.. Thanks, Vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] hessian.mtx----> readable format

Vishal Agarwal wrote: Dear Gromacs Users, Is there a way to convert the hessian.mtx file into a readable format using any of the gromacs utilities? gmxdump -mtx g_nmeig -Justin Any help on this would be highly apprecaited.. Thanks, Vishal --

[gmx-users] gromacs (4.5) installation

Dear experts, I have installed newest version of gromacs (4.5) on our cluster. When I issue the command below to test installation I get an error about atom type CU+2. I am not using such atom type at all! Could you please help me what wrong is. Thanks. grompp -f *.mdp -c *.gro -p *.top -o out >

Re: [gmx-users] gromacs (4.5) installation

Moeed wrote: Dear experts, I have installed newest version of gromacs (4.5) on our cluster. When I issue the command below to test installation I get an error about atom type CU+2. I am not using such atom type at all! Could you please help me what wrong is. Thanks. No one can tell unle

[gmx-users] Re: Restarts: Truncation of file *.xtc failed

Hi Thanks Greg for your answer. Yes, my simulation is in fact pretty long and its files are considerably large. The size of the xtc files is approximately ~2 GB when I am trying to do the restart. I thought on the contrary that my problem was related to another post in today's list ( http://lists.g

RE: [gmx-users] about rdf

> > 1- Actually since I was focusing on rdf for C-C I didnt explain my > > understanding from that post well. Anyway, I have only C and H in the > > system and no protein. You mean I have to make separate groups of C > and > > H for all polymer chains by hand? I trying to find a more smart way > of

Re: [gmx-users] Restarts: Truncation of file *.xtc failed

- Original Message - From: Yongchul Chung Date: Wednesday, September 8, 2010 4:10 Subject: Re: [gmx-users] Restarts: Truncation of file *.xtc failed To: Discussion list for GROMACS users > Hi, > > How big is your file? I assume since you are running 18ps simulation, it > might be

Re: [gmx-users] Re: Restarts: Truncation of file *.xtc failed

- Original Message - From: David de Sancho Date: Wednesday, September 8, 2010 8:04 Subject: [gmx-users] Re: Restarts: Truncation of file *.xtc failed To: gmx-users@gromacs.org > Hi > Thanks Greg for your answer. > Yes, my simulation is in fact pretty long and its files are considerably

Re: [gmx-users] pdb2gmx -chainsep vs -merge

- Original Message - From: nahren manuel Date: Tuesday, September 7, 2010 20:33 Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge To: Discussion list for GROMACS users --- | > Dear Gromacs Users, > > Tsjerk, > > the original

Re: [gmx-users] g_covar & g_anaeig problems

- Original Message - From: Sebastian Breuers Date: Tuesday, September 7, 2010 17:47 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org > Hey, > > taking fewer atoms by ignoring the hydrogens is a good advice. > Thanks a lot. That's just the tip of the iceb

Re: [gmx-users] Tables and forcefield parameters

- Original Message - From: Sai Pooja Date: Sunday, September 5, 2010 8:19 Subject: [gmx-users] Tables and forcefield parameters To: Discussion list for GROMACS users > Hi, > > ques1: > I have 3 energy groups. > I am interested in using tables for LJ and coulomb interactions for > Gr

[gmx-users] GFP Simulation

Dear Gmxers, I am working on a new project and I plan to do some molecular dynamic simulation on an engineered GFP molecule. I have been searching for the parameters for the GFP chromophore without success. Could some one help me? Any reference or parameters will be appreciated. Thanks, Juju

Re: [gmx-users] Tables and forcefield parameters

Thanks Mark :). On Tue, Sep 7, 2010 at 10:06 PM, Mark Abraham wrote: > > > - Original Message - > From: Sai Pooja > Date: Sunday, September 5, 2010 8:19 > Subject: [gmx-users] Tables and forcefield parameters > To: Discussion list for GROMACS users > > > Hi, > > > > ques1: > > I have 3

[gmx-users] Alanine dipeptide simulations

Hi, I am running an npt simulation on alanine dipeptide in explicit solvent using charmm forcefield and tip3p. The pressure is set to 1bar and the barostat is Parrinello-Rahman. The simulation has been running for 45 ns and has not achieved the target average pressure of 1 bar. I don;t understan

RE: [gmx-users] Alanine dipeptide simulations

What pressure has it reached? Probably best graph the pressure versus time plot for the run and show that. I suspect what you are concerned about is the fact that with pressure coupling, the pressure can fluctuation from step to step, very widely, 100s atm is not out of the question. Catc

[gmx-users] reg compilation problem in Mopac gromacs

Dear sir, thanks in advance   When i type the following command in gromacs directory ./configure --with-qmmm-mopac --disable-float it configure successfully but when i compile by make command i got the following error at the end of my compilation 　 libs/libgmxpreprocess_d.a ../mdlib/.libs/libmd_d

RE: [gmx-users] Alanine dipeptide simulations

See http://www.gromacs.org/Documentation/Terminology/Pressure for further details Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304

Re: [gmx-users] Alanine dipeptide simulations

Hi Yes, the fluctuations are large but even the average pressure hasn't converged. Its close 2.5 bar. RMSD ~600 bar. Pooja On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren wrote: > See http://www.gromacs.org/Documentation/Terminology/Pressure for further > details > > > > Catch ya, > > Dr. Dallas

RE: [gmx-users] Alanine dipeptide simulations

Is that really that surprising? You have variations of the order of 100s of bar and are looking for an average that is 1.0 What you are observing is nothing out of the ordinary, from my experience and what others have discussed here on the emailing list. Catch ya, Dr. Dallas Warren M

RE: [gmx-users] Gibbs Energy Calculation, Water/Octanol Partioning

Justin, > Have you tried using the sd integrator? That's what the authors of this paper > used. I don't know if there are stability issues with md vs. sd, but it's a > starting point. That does appear to be the issue. We have repeated the pentane in octanol lambda runs and it completed withou

Re: [gmx-users] Alanine dipeptide simulations

So, what should I aim for when running an NPT simulation? Pooja On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren wrote: > Is that really that surprising? > > > > You have variations of the order of 100s of bar and are looking for an > average that is 1.0 > > > > What you are observing is nothing o

Re: [gmx-users] reg compilation problem in Mopac gromacs

Hi, Please do not cross-post your mailing list questions to individuals unless they have solicited your inquiries. I know nothing about QMMM/MOPAC :-) The best I can suggest is that you haven't made the MOPAC libs available in the default linking path. Please consult whatever installation docum