[gmx-users] Query regarding all-atom simulations on 980 Ti GPUs

Greetings I have just recently started to work on this workstation (details as shown below) and have employed all-atom simulation of 30,000 atoms with this command (just for 1 micro-sec), gmx mdrun -deffnm md -v -ntmpi 2 -ntomp 6 -gpu_id 01 -pin on Running on 1 node with total 8 cores, 16

Re: [gmx-users] md with multiple ligands

Hi Thanh, Maybe try to check if the numbering of your atoms in the topology files is consistent with the .pdb or .gro files they describe. Billy On 1 July 2016 at 09:20, Thanh Le wrote: > > > On Jun 30, 2016, at 3:48 PM, Thanh Le wrote: > > > >

[gmx-users] Failed to lock: pre.log

Hi, I am running a 100ns-REMD with 50 replicas. when continuing the REMD by appending to the old output files, such error happened: "Fatal error:Failed to lock: md1.log. Already running simulation?” Then I had a test of 5 replicas. I limit the run time for 10 minutes for every

Re: [gmx-users] md with multiple ligands

> On Jun 30, 2016, at 3:48 PM, Thanh Le wrote: > > My name is Thanh Le, a graduate student in chemistry. Currently, I am using > gromacs to do a dynamics simulation for my RNA-protein complex. I saw you > posted a question titled “Atoms in the .top are not numbered

Re: [gmx-users] Atoms in the .top are not numbered consecutively from 1

On 6/30/16 6:47 PM, Thanh Le wrote: Hi Gandhi, My name is Thanh Le, a graduate student in chemistry. Currently, I am using gromacs to do a dynamics simulation for my RNA-protein complex. I saw you posted a question titled “Atoms in the .top are not numbered consecutively from 1” on gromacs

Re: [gmx-users] Water molecule can not be settled

Hi, Run with one rank, e.g. gmx mdrun -ntmpi 1 Mark On Thu, Jun 30, 2016 at 6:11 PM zeineb SI CHAIB wrote: > Dear Mark, > > Thank you for your orientation. I looked in Google and based on what you > advised me, I prepared the following mdp file > > integrator = steep >

Re: [gmx-users] Water molecule can not be settled

Dear Mark, Thank you for your orientation. I looked in Google and based on what you advised me, I prepared the following mdp file integrator = steep nsteps = 1000 emtol = 1000.0 emstep = 0.01 energygrps= system pbc = no nstlist = 0 ns-type = simple rlist = 0

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Hi, Best practice is to read and learn others practice from publications that are similar to what you want to do, rather than making ad-hoc changes. In this case, the GROMACS defaults are pretty close to the de facto standard, and supported by analysis work done by other members of the community.

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Dear Justin, Thanks a lot for pointing out the issues. I now understand why there were such high oscillations. Could you please also tell me if there are any ideal values for pme_order and fourier spacing with respect to the cut offs' value of 1.4. Does the following Note imply I can raise the

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

On 6/30/16 9:16 AM, NISHA Prakash wrote: Dear Justin, Thank you for your reply. It is a protein carbohydrate system. Including the solvent, the number of atoms is 43499. I have minimized the system for 200 ps followed by NPT and NVT simulations for 200 ps respectively Given that your

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Dear Justin, Thank you for your reply. It is a protein carbohydrate system. Including the solvent, the number of atoms is 43499. I have minimized the system for 200 ps followed by NPT and NVT simulations for 200 ps respectively Below is the .mdp file. ; VARIOUS PREPROCESSING OPTIONS title

Re: [gmx-users] rmsdist

On 6/30/16 8:58 AM, Sanja Zivanovic wrote: Dear users,Could you please tell me if it is possible to make gmx rmsdist without hydrogens, comparing just heavy atoms? Supply an index file with a group that contains the atoms you want to use. -Justin --

[gmx-users] rmsdist

Dear users,Could you please tell me if it is possible to make gmx rmsdist without hydrogens, comparing just heavy atoms? Thanks in advance a lot Best Regards, Sanja -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

On 6/30/16 8:46 AM, NISHA Prakash wrote: Dear all, I have conducted a 10ns REMD simulation for a protein ligand complex with the temperature range - 270 to 350 K, however the temperature distribution plot of the replicas show that the sampling has occurred at higher temperatures as well that

[gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

Dear all, I have conducted a 10ns REMD simulation for a protein ligand complex with the temperature range - 270 to 350 K, however the temperature distribution plot of the replicas show that the sampling has occurred at higher temperatures as well that is beyond 350K - Below is an excerpt from the

Re: [gmx-users] Tesla K80 vs GeForce GTX 980-repost

Hi, Yes, but it runs the same code. Mark On Thu, Jun 30, 2016 at 2:01 PM Nikhil Maroli wrote: > Thanks, MARK, > > but I saw it is "Pascal." is that new Archi. ? > > > > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] Tesla K80 vs GeForce GTX 980-repost

Thanks, MARK, but I saw it is "Pascal." is that new Archi. ? -- 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

Re: [gmx-users] Treatment of HIE, HID, HIP with the Amber force field

Hi, Only if that makes a sensible model physics... But probably this is a problem in the (user-contributed) port of amber14sb (and there are others, including that they haven't updated the documentation files in it, so it claims to be something else). The alpha carbon has a new type, so probably

[gmx-users] Treatment of HIE, HID, HIP with the Amber force field

Dear Gromacs users, I am running Gromacs using the amber14sb force field. Amber distinguishes histamine residues according to their protonation state into HIE, HID, and HIP. But then Gromacs complains for HID residues: No default Improper Dih. types Do I have to do something additional or should

Re: [gmx-users] Water molecule can not be settled

Hi, Google has some good suggestions for examples for GROMACS mimization in vacuo. You want no PBC, simple grid and maybe no cutoffs. EM has no time, so time step is not a relevant concept. The .mdp option documentation is quite useful... Mark On Thu, Jun 30, 2016 at 12:15 PM zeineb SI CHAIB

Re: [gmx-users] Tesla K80 vs GeForce GTX 980-repost

Hi, Yes, it works already. There's no architectural change that would break things. Mark On Thu, Jun 30, 2016 at 12:01 PM Nikhil Maroli wrote: > HI, > Thanks > > I have seen 1070 is much better than gtx 980ti and cheap also, released ? > but it will support GROMACS or MD?

Re: [gmx-users] Water molecule can not be settled

Dear Mark, Thank you very much for your answer. I'm trying to minimize my protein in vacuo but I'm havig problem to undrstand the concept of "in vacuo" so I'm enable to construct an mdp file and I can't found valid examples in forums and internet. Could you help me with that please? Also,

Re: [gmx-users] Tesla K80 vs GeForce GTX 980-repost

HI, Thanks I have seen 1070 is much better than gtx 980ti and cheap also, released ? but it will support GROMACS or MD? Since it released a few months ago? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before