[gmx-users] RE: micelles and trjconv -pbc cluste

Hi, I've sent the program off list. I hope to have a version compatible with the current or future version of Gromacs and will then upload it to the user contributions. Ran -- Message: 2 Date: Thu, 14 Apr 2011 13:29:42 -0700 (PDT) From: jim jack blhaw...@yahoo.com

[gmx-users] Fwd: genbox

I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atoms at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it add more than atoms than I

Re: [gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Dear GROMACS users, As another check, I simulated the hydration of Sodium ion. The results for the free energy change of un-charging the sodium ion with ffG43a1 force field parameter from q=+e to q=0 in SPC water are the following: 363.3 +/- 2.4 kJ/molin GROMACS 4.0.7 404.7 +/- 1.9

Re: [gmx-users] Re: Trajectory visualization

On Fri, 2011-04-15 at 15:15 +1000, Mark Abraham wrote: On 15/04/2011 3:08 PM, bharat gupta wrote: Reduicng no. of frames means breaking the simulation into smaller frames ... will it affect the result ?? You can use trjconv -dt to reduce the number of frames per unit time, not just

Re: [gmx-users] Fwd: genbox

On 15/04/2011 5:16 PM, leila separdar wrote: I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atoms at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p

[gmx-users] free energy perturbation

Hello, I am doing free energy perturbation for ethane to methanol conversion. Can anybody tell me which of the following way is right to define virtual site for hydrogen? [ virtual_sites2 ] 3 2 1 1 0.00 or [ virtual_sites2 ] 3 2 1 1 1.00 Thanking you in anticipation. With regards,

Re: [gmx-users] Re: Trajectory visualization

Your results are not affected by isualization, are they? Just keep a copy of the original trajectory for analysis. Erik bharat gupta skrev 2011-04-15 07.08: Reduicng no. of frames means breaking the simulation into smaller frames ... will it affect the result ?? On Thu, Apr 14, 2011 at

[gmx-users] Re: micelles and trjconv -pbc cluster

Dear Tsjerk and Ran,  Thanks for the routines you sent me! I will try to apply them as soon as possible. Best regards  George   -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Based on your use of: sc-sigma = 0.3 I wonder what happens with 4.5.3 when you set the env.var. GMX_SCSIGMA_MIN to 0 quoting http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x for free-energy calculations sc-sigma now also sets the minimum soft-core sigma

[gmx-users] Adding water to protein to start the simulation process

Hi User, I have a protein which I have modeled by Homology modelling. The modeled protein has no water molecules in its surrounding environment. How should I add water molecule so that I can start the simulation process? Regards Monisha -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Adding water to protein to start the simulation process

Monisha Hajra wrote: Hi User, I have a protein which I have modeled by Homology modelling. The modeled protein has no water molecules in its surrounding environment. How should I add water molecule so that I can start the simulation process? Please refer to the abundant tutorial

[gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup

Hi gmx-users We have an HPC setup running HP_MPI and LSF/SLURM. Gromacs 4.5.3 has been compiled with mpi support The compute nodes on the system contain 2 x dual core Xeons which the system sees as 4 processors An LSF script called gromacs_run.lsf is as shown below #BSUB -N #BSUB -J

[gmx-users] Energy minimization error

Dear gromacs users, While doing energy minimization for a protein (from pdb), with oplsaa force field and tip4p water model, there was an error and em stopped - Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well

Re: [gmx-users] Energy minimization error

Kavyashree M wrote: Dear gromacs users, While doing energy minimization for a protein (from pdb), with oplsaa force field and tip4p water model, there was an error and em stopped - Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your

[gmx-users] RMSF: Different results for same residue

Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer

Re: [gmx-users] Energy minimization error

Ok thanks On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear gromacs users, While doing energy minimization for a protein (from pdb), with oplsaa force field and tip4p water model, there was an error and em stopped - Fatal error: A

Re: [gmx-users] RMSF: Different results for same residue

Alok Jain wrote: Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for

Re: [gmx-users] RMSF: Different results for same residue

Il 15/04/2011 18:45, Alok Jain ha scritto: Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to

[gmx-users] Pressure coupling problem

Thank you Justin and Peter for your responses. I tried extending the time on the npt equilibration. It helped but not much. My final pressure after the MD run was about 1.15 bar compared to ref_p which was set to 1 bar. Peter, I will try to analyze the potential error using RMSD and Drift.

[gmx-users] Genbox command question

Hello, I'm trying to place 1000 molecules of 1-propanol using CHARMM FF parameters in a -box 6 6 6.   After minimization, I realized that for a single molecule, the potential was slightly above 0, '+24 kJ/mol' to be exact, with electrostatic coloumb potential the greatest contributor.  I used the

Re: [gmx-users] Genbox command question

Fabian Casteblanco wrote: Hello, I'm trying to place 1000 molecules of 1-propanol using CHARMM FF parameters in a -box 6 6 6. After minimization, I realized that for a single molecule, the potential was slightly above 0, '+24 kJ/mol' to be exact, with electrostatic coloumb potential the

[gmx-users] Re: Genbox command question

Thank you Justin. Your explanation really helped. I was actually using 4.0.5, not 4.0.1 (my mistake). Your explanations explained everything very well. Thanks again for your help! On Fri, Apr 15, 2011 at 3:33 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello, I'm trying to

Re: [gmx-users] Adding water to protein to start the simulation process

Monisha Hajra wrote: Hi Justin, I am trying to follow the protocol only. More than the Gromacs own website, I find http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is more useful. Clearly. This is one of many tutorials linked from the site I posted before.

Re: [gmx-users] Adding water to protein to start the simulation process

With all due respect, this is clearly a RT*M moment. * = F Joao Henriques On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Monisha Hajra wrote: Hi Justin, I am trying to follow the protocol only. More than the Gromacs own website, I find

Re: [gmx-users] Adding water to protein to start the simulation process

Indeed :-) 2011/4/16 João Henriques joao.henriques.32...@gmail.com With all due respect, this is clearly a RT*M moment. * = F Joao Henriques On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Monisha Hajra wrote: Hi Justin, I am trying to follow the

[gmx-users] the ligand have more than one molecules

Dear users, Is there anyone has a tutorial of the ligand have more than one molecules? For example: *topol.top:* [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 *ligandname * 3 Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing list

Re: [gmx-users] the ligand have more than one molecules

ahmet yıldırım wrote: Dear users, Is there anyone has a tutorial of the ligand have more than one molecules? Perhaps you can describe in more detail what it is you hope to accomplish. The procedure for dealing with multiple ligands is, in principle, no different from a single ligand.