[gmx-users] clFFT error on iMAC 2017, Gromacs 2019.2, Intel Core i5, GPU Radeon Pro 555 2GB

Hi, Recently I compile new 2019.2 on the new iMAC with GPU Radeon Pro 555 2GB. Below is the compilation: ``` curl http://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz --output gromacs-2019.2.tar.gz tar -xvzf gromacs-2019.2.tar.gz mkdir ~/gromacs cd ~/gromacs-2019.2 mkdir build cd build

Re: [gmx-users] 2019.2 build warnings

Hi Szilárd, We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is most certainly there. Until the issue is solved one way or another, we will be staying with 2018.1, i guess. $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description:    Ubuntu

[gmx-users] Percentage of potential SASA of ligands in Gromacs??

Dear All, How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS. Thank you in advance. Thanks & Regards, [image: Mailtrack]

Re: [gmx-users] REMD - subsystems not compatible

Thanks Mark for reminding me about the existence of the log files. Problem solved, the difference is clearly indicated (number of atoms, my stupid mistake. Cheers /Per > 24 apr. 2019 kl. 16:51 skrev Mark Abraham : > > Hi, > > Generally the REMD code has written some analysis to the log

[gmx-users] GPU kernel code

Hi, How can I see the code of a GPU kernel named nbnxn_kernel_ElecEw_VdwLJCombLB_F_cuda? That exists in src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu however, I can not find its implementation. Can someone help? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Failed to realloc error

Hi, That sort of thing definitely should not happen for systems of size 150k atoms. Can you please upload a .tpr and .log file to https://redmine.gromacs.org so we can investigate? Mark On Wed, 24 Apr 2019 at 15:44, Maxim Brodmerkel wrote: > Hello, > > I encountered an error while working on

[gmx-users] Query regarding capping group "NME"

Dear Gromacs users, I want to capped the end groups of a protein chain with acetyl (ACE) and amine (NME) groups. As I am using gromos96 43A1 force field and NMe is not present in aminoacid.rtp. In amber NME is present but not in gromos. Anyone please suggest something how to generate force

[gmx-users] Failed to realloc error

Hello, I encountered an error while working on simulating the satellite tobacco necrosis virus, comprising 147960 atoms. During the energy minimisation step using GROMACS version 2019.1 I encountered following error: Fatal error: Not enough memory. Failed to realloc 18446744065119617024 bytes

[gmx-users] REMD - subsystems not compatible

Hi gmx-users, I am trying to start a replica exchange simulation of a model peptide in water, but can’t get it to run properly. I have limited experience with REMD, so I thought I’d ask here for all the rookie mistakes it is possible to do. I have also seen the earlier discussions about the

[gmx-users] Updated REMD question

Hello everyone;I have posted a question earlier about REMD simulation but i got no answer so i am going to re-post it with  ore detail hoping someone might give me a hint.  My research focuses on detection and modeling of internal dynamics within proteins. My first attempts with gromacs focused

[gmx-users] What might be the best way of analysis of this kind of salt bridges with Gromacs?

Dear Gromacs users, I have a dimeric protein and I am interested in analysing the salt bridges between chain A and B. When I do this command: *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]* after a while it is killed. I just tryed to do this command using only a frame of trajectory: *gmx

Re: [gmx-users] 2019.2 build warnings

What OS are you using? There are some known issues with the Ubuntu 18.04 + glibc 2.27 which could explain the errors. -- Szilárd On Wed, Apr 17, 2019 at 2:32 AM Alex wrote: > Okay, more interesting things are happening. > At the end of 'make' I get a bunch of things like > > ..

Re: [gmx-users] 2019.2 build warnings

The warning are harmless, something happened in the build infrastructure which emits some new warnings that we've not caught before the release. -- Szilárd On Wed, Apr 17, 2019 at 1:43 AM Alex wrote: > Hi all, > > I am building the 2019.2 version, latest CUDA libs (older 2018 version > works

Re: [gmx-users] Gromacs Benchmarks for NVIDIA GeForce RTX 2080

The benchmark systems are the ones commonly used in GROMACS performance evaluation ADH is a 90k/134k system (dodec/cubic) and RNAse is 19k/24k (dodec/cubic) both setup up with AMBER FF standard setting (referenced can be found on this admittedly dated page: http://www.gromacs.org/GPU_acceleration)

Re: [gmx-users] how can I obtain the potential energy of each atom？

Did you try a script that calls gmx energy in each iteration, parsing the index of each atom as an input??? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of zk_dlut Sent: Monday, April 22, 2019 10:49:25 AM To: gmx-us...@gromacs.org