Re: [gmx-users] Calculation of Static Structure Factor in GROMACS-5.0.7

List of analysis can perform using GROMACS can be found at http://manual.gromacs.org/documentation/2018/user-guide/cmdline.html Highly recommend when you start using GROMACS you read through the entire thing, amazing what you can find that might be useful for your research that didn't even

[gmx-users] Fwd: different vectors from gmx covar and gmx anaeig

Hello, I found out what's going on there, the first set data is the total vector, which I thought was the X component.  Thanks! All the best, Qinghua Forwarded Message --- Subject:different vectors from gmx covar and gmx anaeig Date: Thu, 18 Oct 2018 13:30:13

Re: [gmx-users] Adding residue to .rtp file

Hi, I have added the modified residue entry in the rtp file and able to generate to topology and .gro file. but i got this warning when passing the pdb2gmx command.What is this about? "WARNING: there were 74 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 160

Re: [gmx-users] best force field for small proteins

There isn't really a good answer to that question without more information. If you want all-atom then the standard choices are: OPLS-AA (variants exist) CHARMM (variants exist) AMBER (variants exist) If your protein has a lot of disorder, traditionally, some flavor of AMBER or OPLS would be

[gmx-users] best force field for small proteins

Hello everyone. I wanna to use MD for a protein with about 50 Amino acid and without ligand. what are the best force fields for this purpose? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] reference distance for Lennard Jones interactions

​Hi I have calculated Lennard Jones interaction between drug and Carbon Nano tube by defining "energygroups" and I got the potential by "gmx energy" I have a question, in this figure I have potential versus distance (r), what is the distance? in Lennard Jones equation the distance defines

Re: [gmx-users] How to fix the box size during the simulation?

Hi If your membrane is curved, do you mean to ask how you can enforce membrane *shape* rather than size? If so, fixing the box dimensions may not help maintain shape, depending on curvature morphology involved. Kevin On Thu, Oct 18, 2018 at 5:20 AM lorenaz wrote: > Hi all, > > I am simulating

[gmx-users] different vectors from gmx covar and gmx anaeig

Hello, I am doing PCA analysis to characterize the motion of a domain, I got the files: average.pdb eigenval.xvg eigenvec.trr covar.log Then, with "gmx trjconv -f eigenvec.trr -s average.pdb -o eigenvec.pdb", I got all the vectors in the pdb file "eigenvec.pdb" I also used "gmx anaeig -v

Re: [gmx-users] How to fix the box size during the simulation?

"Is it possible to fix dimensions of the simulation box during the production run?" ---> Of course, simulate in the canonical ensemble (NVT). The isothermal-isobaric ensemble (NPT) employs a barostat, which means that the box volume will have to vary in order to keep the pressure constant. J --

[gmx-users] How to fix the box size during the simulation?

Hi all, I am simulating a protein on a curved membrane and I want the membrane to remain the same size during the whole simulation. Is it possible to fix dimensions of the simulation box during the production run? Best, Lorena -- Gromacs Users mailing list * Please search the archive at