Re: [gmx-users] Spec'ing for new machines (again!)
Gromacs is totally compatible with nvidia based gpu. You need to install cuda drivers and you can build easily with cmake. For amd gpu you would be needing openCL alongwith the sdk for amd gpu. I would suggest you to use nvidia acceleration for better performance. On Sat, Apr 18, 2020, 4:42 AM Alex wrote: > Hello all, > > Hope you're staying safe & healthy! We are starting to spec new machines > and our end goal is two machines, each featuring: > > 1. ~16-18 CPU cores w/hyperthreading > > 2. Four GPUs > > 3. ~256 gigs of RAM. > > A very approximate allocation of money is ~$15-20K per unit, but we > could of course buy more if each machine turns out to be significantly > cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are > welcome. We are somewhat open to AMD-based solutions, but wonder what > the situation is with GPU acceleration, as so far we've been entirely > Intel-based. Will it work with NVIDIA cards? Will we have to install AMD > GPUs? Does current Gromacs perform well on AMD-based rigs? > > Thank you! > > Alex > > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding version of gromacs
I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote: > Dear all, > I have run my simulation on gromacs 5.1.4 for 200ns but now I want to > extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will > there be problem during total simulation of 500ns in my systems. Please > give me suggestion regarding this. > > -- > Ashma Khan > Research Scholar > Department of Chemistry > AMU, Aligarh > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Lincs warning in free energy calculation
Check the forcefield you are using is appropriate for your system or there might be some problem with the ligand parameters. On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani wrote: > Dear Gromacs users > I ran an MD simulation for 3ns and from the last coordinates started a free > energy calculation for 3ns. My system is well equilibrated but after 710725 > steps I am getting Lincs warning every time as below:- > > WARNING: There are no atom pairs for dispersion correction > starting mdrun 'GROtesk MACabre and Sinister in water' > 150 steps, 3000.0 ps. > > Step 710726, time 1421.45 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.03, max 0.23 (between atoms 5470 and 5472) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length >3437 3438 43.80.1080 0.1080 0.1080 > > Step 710726, time 1421.45 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.03, max 0.21 (between atoms 5470 and 5472) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length >3437 3438 43.10.1080 0.1080 0.1080 > > I have added restraints between atoms of ligand and protein and getting > Lincs warning between 1 atom included in restraints as below:- > > [ bonds ] > ;i j type r0A r1A r2AfcAr0B r1B r2B > fcB > *3437* 790810 0.418 0.418 10.0 0.00.418 0.418 10.0 > 41840.00 > > [ angle_restraints ] > ; aiajakal typethA fcAmultA thB fcB > multB > 3437 7908 7906 7908 1100.29 0.01 100.29 418.40 > 1 > 7908 3437 3439 *3437* 1146.50 0.01 146.50 418.40 > 1 > > [ dihedral_restraints ] > ; aiajakal typephiA dphiA fcAphiB dphiB > fcB > 7906 7908 *3437* 3439 1156.16 0.00.0156.160.0 > 418.40 > 7907 7906 7908 *3437* 1-56.93 0.00.0-56.930.0 > 418.40 > 7909 *3437* 3430 3435 1131.32 0.00.0131.32 0.0 > 418.40 > > Can anyone please suggest to me how Should I fix this error? Any help will > be really appreciated. > > Thanks. > > Sadaf > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Faisal Nabi *Pre-Doctoral Fellow (CSIR-JRF)* C/o Professor Rizwan Hassan Khan Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, INDIA. Email-*fn...@myamy.ac.in * * faisalbioc...@gmail.com * Contact no. - *+91-8923713214* -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi, I have been a new user and i was following the protein-ligand complex tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology i have used ATB webserver. I did download the .itp and .pdb file from there and converted that to .gro file. The problem i am facing is it shows an error while i add ions that "Atomtype CAro not found", although i have added the atomtypes in the gromacs topology file still it's showing the same error. I request if somebody could provie me a stepwise protocol i could follow. Thank you -- Faisal Nabi *Pre-Doctoral Fellow (CSIR-JRF)* C/o Professor Rizwan Hassan Khan Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, INDIA. Email-*fn...@myamy.ac.in * * faisalbioc...@gmail.com * Contact no. - *+91-8923713214* -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
