Re: [gmx-users] Using GROMACS with (AMD) OpenCL

If that does not work feel free to share the cmake invocation and cache file and we may be able to figure out something. Cheers, -- Szilárd On Sat, Dec 3, 2016 at 4:02 PM, Gregory Man Kai Poon <gp...@gsu.edu> wrote: > Hi Milan and Szilárd, > > > Many thanks for your comments. So I ins

[gmx-users] Using GROMACS with (AMD) OpenCL

Hello all, I would like to get some practical advice on setting up GROMACS with OpenCL using an AMD GPU (an RX 480 is what I happen to have). The AMD APP SDK indicates that it supports the Catalyst Omega 15.7 driver -- is that compatible to the proprietary Catalyst driver for Linux? Since

Re: [gmx-users] Using GROMACS with (AMD) OpenCL

PRO (on that node with Fury Nano, cause > Debian doesn't have it in its repositories. > If any problem, plaase ask more with some details. > > Best, > > Milan > > On Fri, Dec 02, 2016 at 01:56:03PM +, Gregory Man Kai Poon wrote: >> Hello all, >> >>

[gmx-users] (no subject)

Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water insertion". There is nothing in the online documentation as to how this should be done except a

Re: [gmx-users] gmx convert-tpr problem

00:43 Gregory Man Kai Poon wrote: > Hello all: > > > I am having problems extending my runs using convert-tpr in GROMACS > 2016.1. In the latest instance, for example, I have a 100-ns run that I > want to extend to 200 ns. I used the convert-tpr command to get my new > .tpr fil

[gmx-users] gmx convert-tpr problem

Hello all: I am having problems extending my runs using convert-tpr in GROMACS 2016.1. In the latest instance, for example, I have a 100-ns run that I want to extend to 200 ns. I used the convert-tpr command to get my new .tpr file: gmx convert-tpr -s md_0_100.tpr -until 200 -o

Re: [gmx-users] Possible to extract gro file from a tpr?

Hi Viveca, You could specify in trjconv to output a gro file: gmx trjconv -s md.tpr -f md.xtc -o md.gro ... Would that work? Gregory Get Outlook for Android From: Viveca Lindahl Sent: Friday, March 30, 5:38 AM Subject: [gmx-users] Possible to extract gro file from a

[gmx-users] Simulated tempering

Hi all, I am attempting to do simulated tempering on GROMACS 2016.3.  In my preliminary googling, I have found several questions from different people on the procedure in the past few years but unfortunately without response.  I have read up on the literature on the few papers that described

Re: [gmx-users] Pressure coupling in expanded ensemble simulations

energy methods). Once can always correct the free energy at lambda=1 from NVT to NPT. I Can fill in the details. You do NOT want to do Berendsen for NPT when running expanded ensemble. The results will be incorrect (as I have learned by sad experience_ On Wed, May 8, 2019 at 8:14 AM Gregory Man

Re: [gmx-users] Pressure coupling problem

Hi Ben, Could you try your simulation on another GROMACS build (on a different machine perhaps) to isolate the functional cause of your symptoms? Or perhaps use another FF on the same structure? I think this would be of interest to many users. Best wishes, Gregory On 5/25/2019 5:33 AM,

[gmx-users] trjconv -drop options

Hi all: I am trying to use the gmx trjconv -drop options to pull frames according to criteria in the Y column of an .xvg output (e.g., rmsd.xvg), and I am unable to find documentation beyond the command reference.  It sounds like one specifies the file with -drop and and then use -dropover

Re: [gmx-users] Pressure coupling in expanded ensemble simulations

at 8:06 AM Gregory Man Kai Poon <mailto:gp...@gsu.edu> wrote: Hi Michael, I am just following up on your thoughts on how carrying out expanded ensemble at NVT and converting back to NPT on the mailing list. Again I appreciate your advice in this area. Best wishes, Gregory On 5/8/2019 1

[gmx-users] Pressure coupling in expanded ensemble simulations

Hi all: We are interested to do expanded ensemble simulations (such as simulated tempering) on GROMACS.  Extensive fiddling with the settings and googling on other people's experience suggests that these simulations must use the md-vv integrator, which in turn is compatible with Berendsen or

Re: [gmx-users] Simulated tempering using GROMACS software package (protein+membrane)

Hi Pratiti, There could be several reasons for your temperatures not moving. Assuming that that your mdp options are set up correctly, your weights may be the problem. If they are very far off from optimal, the Monte Carlo may never accept a proposed move. The md.log file should provide

Re: [gmx-users] simulation on 2 gpus

Hi Kevin, Thanks for your very useful post. Could you give a few command line examples on how to start multiple runs at different times (e.g., allocate a subset of CPU/GPU to one run, and start another run later using another unsubset of yet-unallocated CPU/GPU). Also, could you elaborate on

[gmx-users] Failed make check

Hello all, I was trying to install GROMACS 2020.2 and encountered a failed test at make check (#43, mdrun). I pasted what I think is the pertinent snippet below and the full output is in the link: https://www.dropbox.com/s/nfq6yojjdslhxur/make_check.log?dl=0 The cmake incovation was: cmake ..