Re: [gmx-users] lower-end GPUs

maybe GTX 1070 -- 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

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Thanks for the reply Justin. I am just going to use the largest exclusion bond distance I can, then ignore the RDF of those beyond that distance. Seems curious to me (not actually understanding what grommp is generating) that the list is so large. These are linear molecules, 38 atoms, 60

[gmx-users] lower-end GPUs

Hi all, A quick question, likely for Szilárd... Now that we got the taste of very decent GPU acceleration with Titan XP cards, I might be getting a brand new workstation with a 22-core Xeon without any GPUs. We plan to install two GPUs in there and Titan XPs would be too expensive for us in this

Re: [gmx-users] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

The normal use (nrexcl = 3 and fudgeQQ & fudgeLJ > 0) results in GROMACS removing 1-2, 1-3, and 1-4 non-bonded interactions and then adding back scaled to the numbers given. In ClayFF, as I understand it, there is no such exclusion of these 1-x interactions and therefore no 1-4 scaling. If you

[gmx-users] C++ xtc interface

Hello, I would like to do some work with xtc output files, but I'm having trouble. The documentation has the following functions: /* All functions return 1 if successful, 0 otherwise */ extern int open_xtc(XDR *xd,char *filename,char *mode); /* Open a

[gmx-users] RMSD value

Dear users, I have a question regarding the calculation of RMSD value for a big system comprising of many replicas of the same peptide. I know that with RMSD fit you can choose to “superimpose” your reference structure to the one from the trajectory (rot+trans). My question is when supplying

[gmx-users] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

Dear GMX'ers, I have a brief question regarding the use of nrexcl and gen-pairs when used with a non-bonded forcefield, such as ClayFF. I've had a brief look through previous posts but haven't found a completely satisfactory answer. Currently, I have a system that is entirely non-bonded. The

[gmx-users] peptide ligand-protein complex topology

Dear GMX users I want to generate a topology for my peptide ligand, but I dont know if I can use "gmx pdb2gmx -f peptide ligand-protein complex.pdb -o peptide ligand-protein complex.gro -water spce -ignh" ?would you please advice me that how can I generate a peptide ligand topology file? I

Re: [gmx-users] Request to post to gromacs forun

On 01/10/17 17:38, Snijesh VP wrote: Hi Sir, It has been informed to email you to post my questions to the forum. Please do the needful You just did. -- "Work hard in silence let