[gmx-users] g_cluster error

Hello all, I have done two independent GROMACS run for same protein system. I would like to cluster and do further analyses. I used the following commands: 1. g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -f2 md_0_1_noPBC_simulation2.xtc -m rmsd-matrix.xpm Selected '4' for back bone atoms. This p

[gmx-users] gmx potential

Dear All user,I used gmx potential command to obtained electrostatic potential across the DPPE membrane. I think my finding isn't true because there is a peak at the center of bilayer and in the head group there are two maximum that are small and mild in the head group. what is the cause of this

[gmx-users] md simulation of a protein in mixture of water and DMSO

Dear gromacs users, I want to do md simulation of a protein in mixture of water and DMSO molecules. Is it possible with gromacs? How to do it? How to obtain itp file for DMSO? Any help will highly been appreciated. Best, Atila -- Gromacs Users mailing list * Please search the archive at htt

Re: [gmx-users] make a rigid nanoparticle (internally freeze body while it can move as a rigid body )

Hi, This cannot be done with GROMACS, there is no general support for rigid body motion. Mark On Tue, May 22, 2018 at 5:15 PM Samieegohar, Mohammadreza < mohammadreza.sam...@howard.edu> wrote: > Hi > I need to make a rigid Gold nanoparticle to run a coarse grained > simulation. my gold nanopart

[gmx-users] make a rigid nanoparticle (internally freeze body while it can move as a rigid body )

Hi I need to make a rigid Gold nanoparticle to run a coarse grained simulation. my gold nanoparticle will penetrate in a lipid membrane I have built the initial structure by Material studio. This nanoparticle must be a internally freeze body while it can move as a rigid body My question is , how

Re: [gmx-users] Specbond.dat file

Hi, This is all specified in the .rtp file, e.g. with the plus and minus symbols on atoms in the bonds section. Look there and compare with functioning residues. Mark On Tue, May 22, 2018, 12:02 Hemalatha Jayabal wrote: > Hi, > > Thank you. > > When I used pdb2gmx to generate the topology usin

Re: [gmx-users] Specbond.dat file

Hi, Thank you. When I used pdb2gmx to generate the topology using CHARMM, I could see from the bonds section that the bonds were not created between the newly added residue i.e hydroxyproline and the following residue(glycine). But, I also noted that bonds were created between the newly added res

[gmx-users] Free energy and dhdl calculation in Gromacs

Hi all, I am wondering, how is the dh/dl calculated when doing free energy runs in Gromacs. I performed a free energy calculation for ASP deprotonation, from lambda=0 (protonated) to lambda=1.0 (deprotonated) with points 0.0, 0.1, 0.2,…,0.9,1.0, to get dhdl for each lambda. Then I calculated d

Re: [gmx-users] partial exclusion of interactions within 1-4

Hi, That sounds right, given the wording (which I just didn't remember right then). So now that we understand that nrexcl applies to all moleculetypes in the .top then we pick whichever of 1 or 3 is most convenient (probably 1) and add either manual [pairs] or manual [exclusions] to the appropriat

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

Hello Harry, Thank you for the report. It seems to be a trivial error in the code, indeed. It was not caught by the Gromacs automated testing since we don't have Windows + CUDA configuration in it. I have filed a bug report https://redmine.gromacs.org/issues/2509 and this will be fixed in Gromacs

Re: [gmx-users] RDF

Hi Alex, we have at some point looked at this in the group, but results were disappointing IIRC. The approach we tried was basically clustering water in groups of 4, but then you get tripped up by 1) PBC and 2) isolated water molecules in an active site (or something). Either way, this isn't some

Re: [gmx-users] partial exclusion of interactions within 1-4

I feel like I am being tested, but it says what I thought I knew: "defines the name of your molecule in this *.top and nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away." This to me suggests that all coulombic+LJ interactions will be re

Re: [gmx-users] partial exclusion of interactions within 1-4

Hi, What does the documentation of nrexcl in the reference manual say? Mark On Tue, May 22, 2018, 08:51 Alex wrote: > Okay, let me try to rephrase the question, because it seems that I am > definitely unable to make it work and noone's replied so far. > > I have a "molecule" (a periodic boron

Re: [gmx-users] Specbond.dat file

Hej, the specbond.dat file is for extra bonds between non-neighbouring residues (e.g. disulphide bridges). So if you don't need to add anything extra for your residue there if it doesn't do anything like a disulphide would. Cheers Paul On 2018-05-22 09:24, Hemalatha Jayabal wrote: Hi al

[gmx-users] Specbond.dat file

Hi all, I have added a residue (Hydroxyproline) to my .rtp files and have updated the hdb and ffbonded files. While browsing through the manual about specbond.dat, it says that any "special bonds" are to be listed specifically here. Does this mean for the newly added residue also, the bond connect