Re: [gmx-users] (no subject)

There is a minimum number of hydrogen bond formation (2 hydrogen bonds) in my protein-drug complex. I have a question about is there any influence of the drug in my protein-drug complex. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Donors and Acceptors - gmx hbond

Hi all! I've been wondering how donors and acceptors are defined in gmx hbond. In the help output: "(...) OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to

[gmx-users] Potential Shift Verlet

Hi all, I am using the potential-shift-verlet keyword for the coulomb-modifier. I am attempting to find the specific equation for this treatment of the electrostatics. In the manual for the most recent version of Gromacs I found an equation for potential-switch (eq 4.30) but not shift. Is there

Re: [gmx-users] gmx sasa

On 8/9/17 10:00 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir Does anyone know how to measure the SASA energy with unit (kj/mol or kcal/mol) when i give this command: *gmx sasa -f b.trr -s b.tpr -o b.xvg* I got in Y-axix "Area (nm\S2\N)" and when I give this command *gmx sasa -f b.trr

Re: [gmx-users] problem with n2t file

On 8/10/17 2:32 AM, Niko Ukkonen wrote: Hi everyone, I'm trying to write a n2t file for my system, I couldn't find anything in manual, but I read here it is explained in detailed in section 5 in manual. Could you please tell me which page it is? Unfortunately its documentation has been

Re: [gmx-users] Position restrains during alchemical transformation

Hi Mark, thank you for your answer. It works. I used genrestr for generating the position restrains. I now manually edited the respective lines. Gromacs wants only the parameters for the B state (If you repeat the function type you get an error). Eg: 12311000 1000 1000 1000

[gmx-users] (no subject)

Dear Users, I'm determining my .mdp file for NPT equilibration, but I don't know how to determine the ref_p section of mdp. pcoupl = berendsen pcoupltype = surface-tension tau_p = 0.5 0.5 ref_p = 1.0 1.0 compressibility = 4.46e-5 4.46e-5 I'm gonna to calculate surface tension for a layer of

[gmx-users] grompp warning

Hello GMX users, I added another ligand as a new residue in the topology database, and then build the topology of the liand with pdb2gmx, everything worked well. But I got this warning from grompp for a nvt equilibration after successful minimizations: There are atoms at both ends of an

[gmx-users] problem with n2t file

Hi everyone, I'm trying to write a n2t file for my system, I couldn't find anything in manual, but I read here it is explained in detailed in section 5 in manual. Could you please tell me which page it is? Thank you in advance Nikko -- Gromacs Users mailing list * Please search the archive at