[gmx-users] do_dssp

Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The

[gmx-users] g_bundle issue

Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top & bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: ---

[gmx-users] Density question

Dear Gromacs Users, I run an MD simulation of a pure solvent and found out that the density of the solvent deviated a little bit from the actual experimental data. MD density is 880g/ml and the experimental data is 866g/ml. Is this reasonable for toluene solvent molecules. I have a hard

[gmx-users] simulation crashed because of LINCS error

Hello All, With regard to my previous post http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html I have done postion restrained energy minimisation  using  POSRES.itp file obtained from pdb2gmx. so that there should not be any large change in the strucutre of the protein. And after th

Re: [gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie

Hassan Shallal wrote: Dear Gromacs users, I ran a production MD simulation on a ligand in a water box. I used NVT with coloumb and vdw cut-offs and avoided using PME. I analyzed the .edr file using g_lie after the simulation was finished, I found that at all the time steps, the energy was

[gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie

Dear Gromacs users, I ran a production MD simulation on a ligand in a water box. I used NVT with coloumb and vdw cut-offs and avoided using PME. I analyzed the .edr file using g_lie after the simulation was finished, I found that at all the time steps, the energy was 0 KJ/mol, is that normal?

Re: [gmx-users] tip5p in ffcharmm

- Original Message - From: Ramachandran G Date: Monday, May 24, 2010 12:03 Subject: [gmx-users] tip5p in ffcharmm To: gmx-users@gromacs.org > Dear gromacs users,>     I could not able to use tip5p water model with > charmm force field. If anybody tried successfully, please help me.

[gmx-users] tip5p in ffcharmm

Dear gromacs users, I could not able to use tip5p water model with charmm force field. If anybody tried successfully, please help me. Thank you. with regards, Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch

[gmx-users] implicit solvent in CVS

Dear all: I know this question has been asked many times, but it's still tempting for me to ask it again ;-). Could any one suggest a mdp file, including the proper parameter setting, for implicit solvent simulation in gromacs? From all the clues I gathered (the roadmap, the source code),

Re: [gmx-users] Polymer simulation help and suggestions

Caleb Tormey wrote: Justin, Thank you for your response. My simulation will involve around 30 chains of polymer along with varying amounts of different salts. For instance LiPF6, LiClO4 and larger molecules like [1,3-dimethylimidazolium]PF6 and I am looking for the best way to incorporate

Re: [gmx-users] Polymer simulation help and suggestions

Justin, Thank you for your response. My simulation will involve around 30 chains of polymer along with varying amounts of different salts. For instance LiPF6, LiClO4 and larger molecules like [1,3-dimethylimidazolium]PF6 and I am looking for the best way to incorporate these. I guess I am a litt

Re: [gmx-users] tpbconv subset

John Shultz wrote: Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? Modify the .mdp file the way you need to, create a full-system .tpr fi

Re: [gmx-users] tpbconv subset

Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> I want

Re: [gmx-users] tpbconv subset

John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backw

[gmx-users] tpbconv subset

I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file fo

Re: [gmx-users] Polymer simulation help and suggestions

Caleb Tormey wrote: Hello all, I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my poly

Re: [gmx-users] Topology files for OPLSAA and RESP charges

- Original Message - From: "Tanos C. C. Franca" Date: Monday, May 24, 2010 1:03 Subject: [gmx-users] Topology files for OPLSAA and RESP charges To: gmx-users@gromacs.org >    Dear GROMACS users, >    I'm trying to start running jobs using RESP charges > and OPLSAA force field but I am fa

[gmx-users] Polymer simulation help and suggestions

Hello all, I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my polymer from a .pdb file using

[gmx-users] Topology files for OPLSAA and RESP charges

Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and the topology files for the OPLSAA force field. Does someone knows a software to calculate the RESP charges for the ligands and/or, also,

Re: [gmx-users] polymer-topology generation

P.R.Anand Narayanan wrote: Dear users, I am using Gromacs package to run the molecular simulation of a protein that is bonded to a polymer. The polymer I use has around 760 atoms and hence I am not able to generate its .itp and .gro files using PRODRG server. Is there any other way how I ca

Re: [gmx-users] lAM/MPI

- Original Message - From: delara aghaie Date: Sunday, May 23, 2010 18:15 Subject: [gmx-users] lAM/MPI To: gmx-users@gromacs.org --- | > Dear gromacs users, > Our university network is LAM/MPI. >   > I connect to the network from my

Re: [gmx-users] xtc file

- Original Message - From: "Justin A. Lemkul" Date: Sunday, May 23, 2010 13:49 Subject: Re: [gmx-users] xtc file To: Discussion list for GROMACS users > > > Moeed wrote: > >Dear experts, > > > >I am trying to exclude all nonbonded interaction on hexane molecule. > > > > > >1-For the md

[gmx-users] lAM/MPI

Dear gromacs users, Our university network is LAM/MPI.   I connect to the network from my office computer to submit simulation job in gromacs. In order to boot the MPI invironment I use lamboot command. $ lamboot -v lamhosts the lamhosts is a text file where I should introduce the processeros whi

[gmx-users] polymer-topology generation

Dear users, I am using Gromacs package to run the molecular simulation of a protein that is bonded to a polymer. The polymer I use has around 760 atoms and hence I am not able to generate its .itp and .gro files using PRODRG server. Is there any other way how I can generate these files of my po