[gmx-users] g_dipoles, take the normal of the computational box

Dear Gromacs users, I have following question which regards to the g_dipoles tool. In order to get information about the total dipole moment of my protein I wrote following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -o Mtot.xvg -a average.xvg When I looked at the default options, the Z-axi

Re: [gmx-users] g_dipoles, take the normal of the computational box

On 2010-06-04 09.45, Emanuel Peter wrote: Dear Gromacs users, I have following question which regards to the g_dipoles tool. In order to get information about the total dipole moment of my protein I wrote following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -o Mtot.xvg -a average.xvg When

[gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out

Dear Friends I am looking to make the topology of a lipid bonded to a peptide. Although this can be done by defining a new residue in the .rtp, this method may not be the best if I want to repeat the procedure for different residues on the peptide. Is it possible in gromacs to write a patch (like

Re: [gmx-users] Re: acetonitrile from amber to gromacs

hi alan and all others, i love it. i've probably never seen such a helpful and constuctive answer to a question asked over the gmx user mailing list. following your instructions was very informative on the one hand and provided the results that i needed on the other. slightly modifying the the c

[gmx-users] Re: acetonitrile from amber to gromacs

Dear Vedat, Thank you very much indeed. Things only get better with constructive feedbacks, either positive or negative. Glad you're managing well your problem. However, as I see, your problem now is in the tleap level. So, are you in amber mailing list? If so I would suggest to post your questi

Re: [gmx-users] Regarding genconf

jani vinod wrote: Hello, I build a system solvated in water . Then replicated the system using genconf. Now when I am running grompp i am getting following warning Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match (N - C1) Warning: atom name 405 in PH7.top and replicat

Re: [gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out

- Original Message - From: maria goranovic Date: Friday, June 4, 2010 18:51 Subject: [gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out To: Discussion list for GROMACS users > Dear Friends > > I am looking to make the topology

[gmx-users] Adding ideal gases to a simulation

Greetings Gromacs Gurus, I am running a set of simulations, and I want to add Neon and Xenon to my system. I am running OPLS-AA and have found in the ffoplsaa.atp file that parameters for both Neon and Xenon exist. My question boils down to, can I take the information from the ffoplsaa.atp, ffo

Re: [gmx-users] Adding ideal gases to a simulation

On 2010-06-04 15.35, Micholas Smith wrote: Greetings Gromacs Gurus, I am running a set of simulations, and I want to add Neon and Xenon to my system. I am running OPLS-AA and have found in the ffoplsaa.atp file that parameters for both Neon and Xenon exist. My question boils down to, can I tak

[gmx-users] Helix Tilt Calculation

Hi ALL, I am using g_angle to calculate the tilt of individual helix in a rhodopsin GPCR with respect to z axis. In the index file I am defining the top and bottom of each helix with first 4 and last 4 residues of that helix respectively. Strangely, I am getting the tilt angle of the odd helices l

Re: [gmx-users] Helix Tilt Calculation

On Jun 4, 2010, at 4:26 PM, Anirban Ghosh wrote: Hi ALL, I am using g_angle to calculate the tilt of individual helix in a rhodopsin GPCR with respect to z axis. In the index file I am defining the top and bottom of each helix with first 4 and last 4 residues of that helix respectively.

Re: [gmx-users] Adding ideal gases to a simulation

- Original Message - From: David van der Spoel Date: Friday, June 4, 2010 10:06 am Subject: Re: [gmx-users] Adding ideal gases to a simulation > On 2010-06-04 15.35, Micholas Smith wrote: > > Greetings Gromacs Gurus, > > > > I am running a set of simulations, and I want to add Neon and

Re: [gmx-users] Helix Tilt Calculation

Hi, Your 150 degree angle is in reality 30 degrees (180-30). This is a matter of defining the vector representing your helix vs. the direction of the z axis. If your vector points in the opposite direction of the z axis, then your angle will be between 90 and 180 degrees. George Anirban Gho

[gmx-users] PME problem on BG/P cluster

Hello, I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" at Argonne national lab). The simulated system is a box of SPC water with 648,000 atoms and all MD simulations were performed on 256 CPU cores with MPI. The compiling environment was Linux with IBM compiler and

Re: [gmx-users] PME problem on BG/P cluster

- Original Message - From: LuLanyuan Date: Saturday, June 5, 2010 2:01 Subject: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org --- | > Hello, > I got a weird problem by running Gromacs 4.0.7 on a BG/P mac

Re: [gmx-users] PME problem on BG/P cluster

On 2010-06-04 17.49, LuLanyuan wrote: > Hello, > I got a weird problem by running Gromacs 4.0.7 on a BG/P machine > ("Intrepid" at Argonne national lab). > The simulated system is a box of SPC water with 648,000 atoms and all MD > simulations were performed on 256 CPU cores with MPI. The compilin

[gmx-users] How to increase the tolerance for conjugate gradient minimization

Hi, all, Is there a way to increase the tolerance for Conjugate Gradient energy minimization? It seems that I can only get a Tolerance (Fmax) = 1e-4 emtol doesn't seem to do the trick. I tried several values. Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Di

RE: [gmx-users] PME problem on BG/P cluster

Hi, Thanks for all the suggestions. Actually I also tried it without the ativec flag (using the same flags as those on the wiki) and the outcome was the same. I did test it with the fftw3 officially installed on the cluster, and got the same error. Because the problem is related to PME, my firs

Re: [gmx-users] 1-4 interaction not within cut-off

Hi Justin, Thanks for the reply. When I tried to gmxcheck the minimization process I got an error: Timesteps at t=810 don't match (2, 1) Timesteps at t=814 don't match (1, 2) Timesteps at t=816 don't match (2, 1) Timesteps at t=818 don't match (1, 2) till the end of the run, that is why I

Re: [gmx-users] 1-4 interaction not within cut-off

Rabab Toubar wrote: Hi Justin, Thanks for the reply. When I tried to gmxcheck the minimization process I got an error: Timesteps at t=810 don't match (2, 1) Timesteps at t=814 don't match (1, 2) Timesteps at t=816 don't match (2, 1) Timesteps at t=818 don't match (1, 2) till the end of

Re: [gmx-users] 1-4 interaction not within cut-off

Hi Justin Thanks a lot for your prompt reply. The end of the em log file says: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. Steepest Descents converged to machine prec

Re: [gmx-users] 1-4 interaction not within cut-off

Rabab Toubar wrote: Hi Justin Thanks a lot for your prompt reply. The end of the em log file says: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. Steepest Descents c

Re: [gmx-users] Extracting enthalpies during or after MD

Thanks for the help Mark. Just to make sure I understand you correctly, I have a few comments/questions, see below... kind regards, Jesper > - Original Message - > From: li...@jsx.dk > Date: Friday, June 4, 2010 10:35 > Subject: Re: [gmx-users] Extracting enthalpies during or after MD > T

Re: [gmx-users] 1-4 interaction not within cut-off

Well all the relevant info from m&m is attached below. I tried to contact the author with no reply!. Ref: Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 27, Issue Number 4, (2010) "The GROMACS 3.3.3 simulation package (www.gromacs.org) was used for all the simulations with

Re: [gmx-users] 1-4 interaction not within cut-off

Rabab Toubar wrote: Well all the relevant info from m&m is attached below. I tried to contact the author with no reply!. Ref: Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 27, Issue Number 4, (2010) "The GROMACS 3.3.3 simulation package (www.gromacs.org) was used for al

Re: [gmx-users] Constraint causing system to explode

OK, I've done as Mark suggested, replaced the type 2 constraint between the amino terminal nitrogen atom and the C-terminal carbon atom with a type 6 bond, r0=0.8, r1=0.8, r2=1, which acts as a distance restraint. This has run clean without crashing for 1.6 ns of simulation on a single processo

Re: RE: [gmx-users] PME problem on BG/P cluster

- Original Message - From: LuLanyuan Date: Saturday, June 5, 2010 5:04 Subject: RE: [gmx-users] PME problem on BG/P cluster To: gmx-users@gromacs.org --- | > Hi, > Thanks for all the suggestions. > Actually I also tried it

Re: [gmx-users] 1-4 interaction not within cut-off

Rabab Toubar wrote: they are stating explicitly that it is a twin range cutoff the manual states that "vdwtype: Cut-off Twin range cut-off’s with neighbor list cut-off rlist and VdW cut-off rvdw, where rvdw ≥ rlist." "coulombtype: Cut-off Twin range cut

Re: [gmx-users] Extracting enthalpies during or after MD

- Original Message - From: li...@jsx.dk Date: Saturday, June 5, 2010 5:58 Subject: Re: [gmx-users] Extracting enthalpies during or after MD To: Discussion list for GROMACS users > Thanks for the help Mark. Just to make sure I understand you > correctly, I > have a few comments/question

Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization

- Original Message - From: Arthur Roberts Date: Saturday, June 5, 2010 4:57 Subject: [gmx-users] How to increase the tolerance for conjugate gradient minimization To: gmx users > Hi, all, > > Is there a way to increase the tolerance for Conjugate Gradient > energy minimization? > >

Re: [gmx-users] Constraint causing system to explode

- Original Message - From: Warren Gallin Date: Saturday, June 5, 2010 7:02 Subject: Re: [gmx-users] Constraint causing system to explode To: Discussion list for GROMACS users > OK, I've done as Mark suggested, replaced the type 2 constraint > between the amino terminal nitrogen atom a

Re: [gmx-users] Extracting enthalpies during or after MD

Aaah, I get it now (finally)... Thanks again... Jesper > > > - Original Message - > From: li...@jsx.dk > Date: Saturday, June 5, 2010 5:58 > Subject: Re: [gmx-users] Extracting enthalpies during or after MD > To: Discussion list for GROMACS users > >> Thanks for the help Mark. Just to ma

[gmx-users] equilibration + Segmentation fault

Hello, I am trying to equilibrate my system, ionic liquids. My simulations gets stop immediately. I reduced the step size. I modified initial structure. I changed the box size. I checked force field parameters. I am using opls foce field. I repeated my energy minimization 2-3 times. I could not

Re: [gmx-users] equilibration + Segmentation fault

Nilesh Dhumal wrote: Hello, I am trying to equilibrate my system, ionic liquids. My simulations gets stop immediately. I reduced the step size. I modified initial structure. I changed the box size. I checked force field parameters. I am using opls foce field. I repeated my energy minimizati

Re: [gmx-users] equilibration + Segmentation fault

I am using the opls parameters from Lope's paper. In vaccum energy minimzatin is working well. MD is not at all working. My other systems are running well. In the present system I changed the anion, cation parameters are fine. Is the problem with anion parameters? Nilesh On Fri, June 4, 2010 10:

Re: [gmx-users] equilibration + Segmentation fault

Nilesh Dhumal wrote: I am using the opls parameters from Lope's paper. In vaccum energy minimzatin is working well. MD is not at all working. My other systems are running well. In the present system I changed the anion, cation parameters are fine. Is the problem with anion parameters? If it

[gmx-users] taking snapshots of the protein after simulation

Dear Gromacs users, I have had one of my studied proteins simulated in a 5 ns production. Now, I wonder how can I get, let's say, 100 coordinates files, each file represent the coordinates of the protein at certain time during the simulation, for example, each 50 ps OR.. What if I want these 10

Re: [gmx-users] taking snapshots of the protein after simulation

Hassan Shallal wrote: Dear Gromacs users, I have had one of my studied proteins simulated in a 5 ns production. Now, I wonder how can I get, let's say, 100 coordinates files, each file represent the coordinates of the protein at certain time during the simulation, for example, each 50 ps OR

[gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD

Dear Gromacs and VMD users. I am trying to visualize a simulation in which a small molecule is interactiong with a protein in a water box. The simulation has been produced using gromacs. I am using VMD for that purpose. I use the .gro and the .xtc files to load the trajectory to the VMD. What

Re: [gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD

- Original Message - From: Hassan Shallal Date: Saturday, June 5, 2010 13:52 Subject: [gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD To: gmx-users@gromacs.org Cc: vm...@mailhost.ks.uiuc.edu --

Re: [gmx-users] taking snapshots of the protein after simulation

- Original Message - From: Hassan Shallal Date: Saturday, June 5, 2010 13:16 Subject: [gmx-users] taking snapshots of the protein after simulation To: gmx-users@gromacs.org --- | > Dear Gromacs users, > > I have had one o

[gmx-users] Topology Generation

Hello All, I have to do simulation on one of the protein which contains one dioxy group, as gromacs do not have information to generate toplogy for it, I tried it with PRODRG, but is giving error: ERRDRG> PRODRG does not deal with mono/di-atomic molecules. PRODRG> Program terminated unsuccessful

RE: [gmx-users] taking snapshots of the protein after simulation

Hi Mark, Thanks alot for the sound and deep advice, I caugth what you meant by design should not be only for the experiment but also for the data analysis even before collecting the results... Once again thanks Hassan From: gmx-users-boun...@gromacs.org on