Re: [gmx-users] Preparing a silicon bulk

Thanks for the reply. I am quite new to the field of Materials so I do need someone else to find a “good” paper on parameters for a silicon surface. While I am waiting to for that, I am actually very curious that why gromos does not have such parameters and nearly all popular forcefields (for b

[gmx-users] a question about Electric fields

hello all I have some questions about add a voltage to a membrane with a protein system 1, how could i add a such as 30mv Electric fields in Z-axis(along the pore) 2, i used the Electric fields in mdp file to define Electric fields(E-z,0.03mv/nm) in z-axis but the subunit(five subunits in a protein)‍

[gmx-users] Postdoctoral position at the KAUST

Subject: Postdoc position in Computational Biology/Bioinformatics Employer: KAUST - King Abdullah University of Science and Technology From: Prof. Luigi Cavallo Kaust Catalysis Center Physical Sciences and Engineering Division King Abdullah University of Science

Re: [gmx-users] Problems with CO2-water simulation

On 2014-12-14 09:49, sujithkakkat . wrote: Dear all, There is something which I missed to include, which I think is adding to the confusion regarding the positive energy values. The OPLSAA topology of methane which is available in Dr Justin Lemkul's Gromacs tutorial ( http://www.bevanl

Re: [gmx-users] Non-bonded interactions

On 12/20/14 9:12 AM, Doa Hawamdeh wrote: Dear All, I want to use GROMACS 5.0.3 to simulate charged groups in my system, what are the types of the nonbonded interactions (lennard-Jones and coulomb) that I have to use?? All biomolecular force fields in Gromacs were parametrized to include LJ

Re: [gmx-users] Element naming format in .pdb file

On 12/20/14 12:12 AM, Rajan Kumar wrote: Dear all, I am trying to study wetting of Graphene oxide. I have prepared a structure file using material studio, which I will simulate in GROMACS. My structure contain some epoxy and hydroxyl functional group in Graphene sheet. However, the structure

Re: [gmx-users] Preparing a silicon bulk

On 12/20/14 5:29 AM, Kevin C Chan wrote: Thanks for the reply. In principle that is what I plan to do - generate a basic topology (with homogeneous charge information) and then manually (or a script) change the charge of each SI atom. Honestly I only have experience of writing a simple topolog

[gmx-users] Non-bonded interactions

Dear All, I want to use GROMACS 5.0.3 to simulate charged groups in my system, what are the types of the nonbonded interactions (lennard-Jones and coulomb) that I have to use?? Thank you. Doa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_

Re: [gmx-users] Pressure in gromacs

As long as your GRA sheet is in the XY plane (as you are applying force from Z direction), your method to apply pressure and the formula for its calculation seems correct to me. --narendra -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/

Re: [gmx-users] Element naming format in .pdb file

may be try both ways in a small file. feed it to pdb2gmx and then check the topol.top file to see if it uses the correct forcefield name? On Sat, Dec 20, 2014 at 12:12 AM, Rajan Kumar wrote: > Dear all, > > I am trying to study wetting of Graphene oxide. I have prepared a structure > file using

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 91

Thanks for the reply. In principle that is what I plan to do - generate a basic topology (with homogeneous charge information) and then manually (or a script) change the charge of each SI atom. Honestly I only have experience of writing a simple topology for a MARTINI system. So what I expect w