Re: [gmx-users] OPLS parametrizaton

Em 02-04-2011 0:33, Justin A. Lemkul escreveu: Marcelo Silva wrote: Hi, I am trying to simulate mixtures of ethanol and trifluoroethanol and I would like to use the same parameters used on OPLS parametrization. On the OPLS1996 paper the authors starts by stating that they've used

[gmx-users] OPLS parametrizaton

Hi, I am trying to simulate mixtures of ethanol and trifluoroethanol and I would like to use the same parameters used on OPLS parametrization. On the OPLS1996 paper the authors starts by stating that they've used 267 molecules and "The box size varied from approximately 26 26  26 Å for met

Re: [gmx-users] # Protein non-integer charge‏

Thank you Justin, that was exactly the problem. When I ran pdb2gmx in another computer it worked fine. I must have changed the .rtp file. Best regards, Marcelo Em 07-03-2011 15:14, Justin A. Lemkul escreveu: Marcelo Silva wrote: The pdb command was: pdb2gmx -f prot.pdb -o

[gmx-users] # Protein non-integer charge‏

Hi everybody, My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia cenocepacia J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure. In order to refine the structure, I am now using in Gromacs the pdb file

Re: [gmx-users] Position restraint problem

Thank you Justin and Mark for your help. The problem is that I wasn't using the .gro file from the minimization step and it was giving a segmentation fault problem too, but I've corrected that problem, ran the simulated annealing without constraints and it worked fine. But I have another quest

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

I don't know if this could be the issue, but are you sure that after the energy minimization step you are using the .gro file you've obtained? I'm telling you this because once I forgot to put it on the following nvt equilibration: grompp -f nvt.mdp -c *em.gro* -p topol.top -o nvt.tpr and I go

[gmx-users] Position restraint problem

Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tried to restrain the posi

Re: [gmx-users] perfluorohexane pdb... again

Angél, I'm sending you my initial pdb in attachment. I chose the box size to fit the experimental density. I am just trying to get simple properties of the pure compounds hexane and perfluorohexane and of a mixture 0.5 hexane/perfluorohexane (density mainly). But maybe I just need a long molec

RE: [gmx-users] perfluorohexane pdb... again

I'm sorry to send another message but the sa.mdp file I sent was an old one Best regards From: jokle...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] perfluorohexane pdb... again Date: Tue, 11 Jan 2011 17:44:50 + Hello Angél, I started with hexane just to know what

Re: [gmx-users] perfluorohexane pdb... again

Thank you Angél and Stephane for your help I also have another question. Using the pure hexane pdb (I am mixing hexane and perfluorohexane), I've run simmulated annealing with a box of 500 molecules trying to obtain a good conformer distribution. The heating steps were: time (ps): 0 8 50 58

[gmx-users] Perfluorohexane

Hi everybody, I was looking for the structure of perfluorohexane to create the pdb file to use with gromacs but I can't find anywhere. I have also looked in pdb databases. Do you know any paper where the structure is reported? Is it possible to use gromacs to do the geometry optimization? Tha

Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study

Thank you Mark, But in the case of trifluoroethanol: C(F) 0.53231 F -0.20571 F -0.20571 F -0.20571 C(H) 0.12632 H(C) 0.08252 H(C) 0.08252 O -0.63512 H0.42862 The total charge is zero,

[gmx-users] Trifluoroethanol-Ethanol mixtures study

Hi everybody, I am starting to simulate ethanol-trifluoroethanol mixtures with opls aa, but TFE is not defined in the opls rtp file, so I added a new entry. I would like to confirm if the way the charge groups are defined for ethanol are mantained for TFE: CB 1 HB11 HB21 HB3

Re: [gmx-users] Add gromacs forcefield w/ virtual site

Thank you Chris for your answer: 1) The molecule has no net charge because the virtual site in the center of mass is a point charge twice the charge in the O atom. 2) Until now I've created 5 files but I don't know if I am doing the right thing: * forcefield.itp #define _FF_OXY [ defau

[gmx-users] Add gromacs forcefield w/ virtual site

I am trying to simulate oxygen using gromacs but there seems to be no forcefield parameters for this molecule. So I would like to add a forcefield to gromacs which is a 3 site model: The two oxygens are lennard jones particles and there's a point charge at the center of mass. The reference a