[gmx-users] Hydrophobic interactions and electrostatic interactions between the protein chains

Hi dear GROMACS usersI want to calculate  hydrophobic interactions and electrostatic interactions between the protein chains using gromacs trajectory  . Please guide me.Thanks a lot -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] VMD movie making-remove water molecules from .trr after a simulation

Thank you Justin. Is it possible to choose protein and ligand separately (e.g. 1|13) in the trjconv, since I chose protein-ligand subgroup which was taken as a whole and ligand can not be distinguished individually ? Or should I do any modifications in VMD ?  On Monday, March 11, 2019,

Re: [gmx-users] gmx trjconv trr xtc

.trr and .xtc are two different file formats, with the latter being compressed. Therefore, an .xtc file will be significantly smaller than a .trr Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade,

[gmx-users] gmx trjconv trr xtc

Dear groamcs user, A system of mine contains two molecule type of A and B in water. Using gmx trjconv -f out.xtc -o out.last.5ns.trr I first truncated the last 5ns of the system's XTC file as a TRR file and just selected the non-water contents so that the TRR file only has A and B. The TRR file

Re: [gmx-users] VMD movie making-remove water molecules from .trr after a simulation

On 3/11/19 6:01 PM, mary ko wrote: Dear all How can I make a movie from a protein-ligand simulation in VMD? I opened complex.pdb and md-fit.trr and  the movie is shown but due to the large number of water molecules it freezes after some frames. How can I remove solvent molecules from the

Re: [gmx-users] gromacs error in vacuum preparation simulation

On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote: If i don't use -maxwarn option they send me the same error. Omitting -maxwarn won't fix problems, but it is a very bad habit to casually use -maxwarn as it overrides critical problems with your input. I see also this: WARNING 1

[gmx-users] VMD movie making-remove water molecules from .trr after a simulation

Dear all How can I make a movie from a protein-ligand simulation in VMD? I opened complex.pdb and md-fit.trr and  the movie is shown but due to the large number of water molecules it freezes after some frames. How can I remove solvent molecules from the md-fit.trr? Any other suggestions how to

Re: [gmx-users] gromacs error in vacuum preparation simulation

If i don't use -maxwarn option they send me the same error. I see also this: WARNING 1 [file topol.top, line 23986]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform

Re: [gmx-users] gromacs error in vacuum preparation simulation

On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote: Hi everybody I want to do one dynamic simulation of one protein i'm try to minimize the protein in vacum before the simulation runing but gromacs send me this error: --- Program:

[gmx-users] gromacs error in vacuum preparation simulation

Hi everybody I want to do one dynamic simulation of one protein i'm try to minimize the protein in vacum before the simulation runing but gromacs send me this error: --- Program: gmx grompp, version 2018.6 Source file:

Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system

Hi, Mark, I'd be happy to, as soon as I get a chance. I know very little about how GROMACS works internally, but I had a few ideas I wanted to share in the hopes that they might help. One is that pairwise parameters for electrostatics could be implemented in the same way that LJ parameters are

Re: [gmx-users] gmx analyze -av

On 3/11/19 2:08 PM, Amin Rouy wrote: Hi, I notice that the flag ''-av'' in gmx analyze does not give the average value of the set, rather the data file itself. As it should. From gmx help analyze: "Option -av produces the average over the sets." If you want the average of different

[gmx-users] gmx analyze -av

Hi, I notice that the flag ''-av'' in gmx analyze does not give the average value of the set, rather the data file itself. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite

Thanks a lot, Kevin for your comments and help. Zeineb -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] Build a .top file

Hello, So i'm starting to learn about MD simulations and i've done the tutorial of Lysozyme in Water for Gromacs, my work is to do MD simulations for sugars using the tool do_glycans and the force field Glycam06, however i don't know how to generate the .top file? i would appreciate it if you

[gmx-users] pinoffset w LINCS error

Hi, I have two servers with AMD2950X (16 physical cores). One with 16Gb RAM and RTX2080Ti, the other 32Gb RAM and GTX1080Ti. I use gromacs 2018.3, compiled on the same way on both of the servers. I wanted to run two simulations on the same host (8+8cores and GPU0 and GPU1). They are OK on

[gmx-users] Gomacs 2019 build on sles12 and centos

Hi All, I've built Gromacs 2019 on both a CentOS 7 and SLES12 machine. Built using gcc@7.2.0 Dependencies: fftw@3.3.8 openmpi@3.1.3 When running "make check" on both machines, I'm getting the same timeout error for test 29 - see below for extract and attached for full test output anyone got any