Re: [gmx-users] Videocard selection

3500 cores vs 4500 cores and See http://hwbench.com/vgas/geforce-rtx-2080-ti-vs-geforce-gtx-titan-xp And https://gpu.userbenchmark.com/Compare/Nvidia-Titan-Xp-vs-Nvidia-RTX-2080-Ti/m265423vs4027 However, if you must have support, then it must be titan -Original Message- From:

Re: [gmx-users] Pore size calculation

If you actually can model water in the pore, then run a few experiments changing the VDW radius of the water oxygen. This will give you the limiting size of the pore and this is the parameter you actually need to know. -Original Message- From:

Re: [gmx-users] Pore size calculation

Rahul, What do you mean by pore size? A hole in the membrane caused by external tension ? The space occupied by the protein ? Does lipid occupy the walls of the pore ? Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of RAHUL SURESH Sent:

Re: [gmx-users] Itp for a longer molecule out of a shorter one

Alex, Having the itp for the shorter molecule you have most of what you need. Use x2top to create the top file for the longer molecule. Adjust, if necessary, the atomname2type.n2t file in the ff file to create any necessary atom types being sure to select the proper ff. Charges, bond lengths

Re: [gmx-users] Performance of GROMACS on GPU's on ORNL Titan?

For what it is worth: on our AMD 2990wd 32 core, 2 x 2080ti we can run 100k atoms at ~ 100ns/day NVT , ~ 150 ns/day NPT so 8 -10 days to get that microsecond. I'm curious to learn what kind of results you might obtain from Oak Ridge and if the cost/clock time analysis makes it worthwhile. Paul

Re: [gmx-users] Gromacs 2018.5 with CUDA

-Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Thursday, January 31, 2019 7:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Gromacs 2018.5 with CUDA On Wed, Jan 30, 2019 at 5:14 PM wrote: > > Vlad, > >

Re: [gmx-users] (no subject)

Run the tutorials -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Satya Ranjan Sahoo Sent: Wednesday, January 30, 2019 11:19 PM To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Sir, I am a beginner to GROMACS. I was unable to understand

Re: [gmx-users] Gromacs 2018.5 with CUDA

Vlad, 390 is an 'old' driver now. Try something simple like installing CUDA 410.x see if that resolves the issue. if you need to update the compiler, g++ -7 may not work, but g++ -6 does. Do NOT install the video driver from the CUDA toolkit however. If necessary, do that separately from

Re: [gmx-users] how can I get two parallel lysin in the same box?

Giuseppe, Use Avogadro, import or construct the four ( if I understand your model ) molecules in the desired orientations. Save as a pdb. Used editconf to construct the box. Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Giuseppe R Del

[gmx-users] modeling evaporation NVP NVE

Dear Users, I am trying to understand a model of water evaporation and am asking for a few of suggestions or just point to a link. So far I have modeled 1 molecules of spce water and equilibrated to a density near 1 gm/cc. I then double the size of the box and then using

Re: [gmx-users] multiple GPU usage for simulation

I am not expert on this subject but have recently gone through the exercise... Firstly, does nvidia-smi indicate both cards are active ? Secondly, for the nvt or npt runs have you tried mdrun commands similar to : mdrun -deffnm file -nb gpu -gpu_id 01 or mdrun -deffnm file -nb gpu -pme

Re: [gmx-users] use of DPOSRES without pdb2gmx

Justin, Thanks, Bartimaeus -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Thursday, January 17, 2019 2:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] use of DPOSRES without pdb2gmx On 1/17/19 3:33 PM,

[gmx-users] use of DPOSRES without pdb2gmx

Dear Users, Suppose you do not use pdb2gmx and therefore do not use the -I option for all constraints. Suppose further you do not generate a restraint file for the non-protein molecules in the model. Then what effect, if any, does setting constraints = all-bonds or h-bonds have ? Thanks

Re: [gmx-users] Results of villin headpiece with AMD 8 core

Mirco, Here are the results for three runs of the million atoms DPPC ===8 core 2700x 1080ti == gmx mdrun -deffnm dppc.md -nb gpu -pme gpu -ntmpi 4 -ntomp 4 -npme 1 -gputasks Core t (s) Wall t (s) (%) Time: 5286.270 330.392 1600.0

[gmx-users] Results of villin headpiece with AMD 8 core

Dear Users, For those of you considering a workstation build and wonder about AMD processors I have the following results using the included npt and log intro for the villin headpiece in ~ 8000 atoms spc/e. The npt was run from a similar nvt ( 10 steps ) . The best results were achieved

[gmx-users] AMD 32 core TR

Dear users, I had trouble getting suitable performance from an AMD 32 core TR. By updating all the cuda drivers and runtime to v10 and using gcc,g++ -6 from v5 -- I did try gcc-7 but Cuda 10 did not appreciate the attempt -- and in particular removing CUDA v7 runtime.), I was able to

Re: [gmx-users] Large system

As suggested, compare the number of molecules/atoms implied in your top file against that in your gro/pdb file. This is one aspect of Gromacs that it never gets wrong. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Bratin Kumar Das Sent:

Re: [gmx-users] error on opening gmx_mpi

Thank you - both - very much again. The "mpir_run -npx gmx -mdrun." command was lifted from a Feb 2018 response from Szilard , to a multi gpu, user which he used as an example. I'll crank on your pointers right now. Paul -Original Message- From:

Re: [gmx-users] using dual CPU's

Thank you again, "I'll be back" when I sort all this out. Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Monday, December 17, 2018 1:16 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] using dual

Re: [gmx-users] using dual CPU's

Carsten, A possible issue... I compiled gmx 18.3 with gcc-5 ( CUDA 9 seems to run normally ) Should recompile with gcc-6.4 ? Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of p buscemi Sent: Thursday, December 13, 2018 1:38 PM To:

Re: [gmx-users] using dual CPU's

Szilard, I get an "unknown command " gpustasks in : 'mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING where > typically N = 4, 6, 8 are worth a try (but N <= #cores) and the > TASKSTRING should have N digits with either N-1 zeros and the last 1 > or N-2 zeros and the last two

Re: [gmx-users] using dual CPU's

Dear users ( one more try ) I am trying to use 2 GPU cards to improve modeling speed. The computer described in the log files is used to iron out models and am using to learn how to use two GPU cards before purchasing two new RTX 2080 ti's. The CPU is a 8 core 16 thread AMD and the GPU's

Re: [gmx-users] generic hardware assembling for gromacs simulation

Seke, Yes, you can do a build with the components you have. The I5 ( 4760 ?) with 4 cores and no other threads is not particularly fast but should work The 1050 has some 640 or 768 cores depending on the version and will produce approximately a factor of 5x over the CPU alone. You will need at

[gmx-users] FW: Re: Re: liquid-solid/liquid-air interface simulations

Dear gmx users, I ran across this 2016 response mentioning titania. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/105969 .html I am familiar with Gromacs using it to model protein adsorption onto polymers. Now I need to look at a film drying on TiO2. What I have

Re: [gmx-users] force field not found

Alex, Justin, I've managed to make and run polymers using Avogadro ,modifying the n2t, then creating the top using x2top under 54a7 ff. The method may be useful for others but before presenting it to the user group, it should be reviewed so that glaring mistakes/concepts are revised.

Re: [gmx-users] atom types not found

Alex, This pertains the prior correspondence to building a polymer and is the process I've been developing. To date I can obtain an ITP and pdb from ATB for a monomer. From there with information in those files, it is relatively easy to construct the n2t file to use in x2top. ( I’d be

Re: [gmx-users] (no subject)

Have you tried the "insert-chemicals-after-md" command ? PB > On Jul 11, 2018, at 4:50 AM, Mark Abraham wrote: > > Hi, > > Are you trying to observe something about the transition, or merely the > different end points? > > Mark > >> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar wrote: >>