[gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)"

Hello! So I am doing my B.Tech thesis on studying the diffusion coefficients of alkanes at infinite dilution in water. I am using TraPPE-UA model for alkanes and TIP4P/2005 representation for water solvent. The problem is pretty simple but the simulations don't seem to run. I am currently working

[gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)"

Hello! Ignore the last mail. So I am doing my B.Tech thesis on studying the diffusion coefficients of alkanes at infinite dilution in water. I am using TraPPE-UA model for alkanes and TIP4P/2005 representation for water solvent. The problem is pretty simple but the simulations don't seem to run.

Re: [gmx-users] electric field

Dear Maryam, You can make use of mdrun's -field option, and inspect its output. I have had situations where a static field hasn’t worked the way I expected it to, so it is generally a good idea to check just to be sure. It is usually enough to just run the simulation for a few steps, inspect th

Re: [gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)"

Hi, I would start my removing the last unconnected line (l. 35) from forcefield.itp and try again. Regards, Peter From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Shantanu Singh [si

Re: [gmx-users] difference between entropic energy and free energy

On 11/15/15 10:20 PM, Ming Tang wrote: Deer list, I am quite confused about the concept of entropic energy and free energy. Could anybody help to tell me what is the difference between them? Try Google or any undergraduate physical chemistry textbook. This is not the right forum for such

[gmx-users] g_select problem

Hello: I would like to calculate the number of water molecules within 4A of residues number 400, and I try to run it with command: g_select_mpi -f input.gro -sinput.gro -os water.xvg -sf selection.dat here is my selection.dat: waterO = resname SOL and name OW; p = resnr 400 and Protein; clo

Re: [gmx-users] electric field

Hi, I can confirm electric field (even laser-pulse form) in GROMACS (all version from 3.0 to current newest one) work fine. To check it, you may consider a system containing only an ion (say Na+) in vacuum and set mdp file as: ### dt = 0.0002; ps ! nsteps =

[gmx-users] SASA: Gromacs5 vs Gromacs4

Hi I'm having some trouble in reproducing SASA values of Gromacs 4 with Gromacs 5. Instead of giving the surface and output group via the command line I have tried to use the -surface and -output option but the results differ. The difference is not huge but still there. Any idea what I am doing wr

Re: [gmx-users] SASA: Gromacs5 vs Gromacs4

On 11/16/15 10:18 AM, morpheus wrote: Hi I'm having some trouble in reproducing SASA values of Gromacs 4 with Gromacs 5. Instead of giving the surface and output group via the command line I have tried to use the -surface and -output option but the results differ. The difference is not huge bu

Re: [gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)"

Thanks peter. Kind of worked out. There's some small issues left which I'll be able to resolve hopefully. Thanks a lot. On Mon, Nov 16, 2015 at 3:22 PM, Peter Stern wrote: > Hi, > > I would start my removing the last unconnected line (l. 35) from > forcefield.itp and try again. > > Regards, > P

[gmx-users] Ligand Virtual Sites

Dear GMX users, I am trying to generate a custom virtual site for a C-NH3 group of a ligand. As a first test, I would like to use the parameters of the Lys virtual site, but I can't see how the coordinates of the dummy atoms are generated (I have already checked the tutorial and the gromacs manual)

Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun

Dr. Lemkul Thanks for your reply. However , I used npme = 0 and could then utilize 64 processes. I did a NPT equilibration with Berendsen thermostats / barostats and found after 5 ns the density to be 999 kg/cu m and average press = 0.4 bar. There was marginal drift. Are these artifacts or I need

Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun

Hi, On Mon, Nov 16, 2015 at 7:50 PM Agnivo Gosai wrote: > Dr. Lemkul > > Thanks for your reply. > However , I used npme = 0 and could then utilize 64 processes. I did a NPT > equilibration with Berendsen thermostats / barostats and found after 5 ns > the density to be 999 kg/cu m and average p

[gmx-users] Select waters in a specific pore with gmx select

Dear all How can i select water molecules between a specific residue in the top and another residue in the bottom of a specific pore in the tetramer AQP5? I used gmx select but i couldn't find the proper expression to select it. -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Computing of reaction coordinate by g_wham

Dear Gromacs users, please, is there someone that can help me to understand how g_wham compute the reaction coordinate of pulled group? I would like to compute the PMF for the passage of a molecule through a channel (with spatial restraint) using the umbrella sampling (US) technique. I built the