[gmx-users] Energy minimization issue

Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has stopped, but the forces have not converged to the*

[gmx-users] new i9 processor

BS”D Dear All, The new Skylake-X CPU’s have very high core counts, and could, in theory, take the place of a two socket 16 core Xeon system. One could create a machine as follows: 1 x Core i9 7960X with 16 cores 2 x Geforce 1080 graphic cards, and run a simulation with 2 MPI ranks, couplin

Re: [gmx-users] Walls and center of mass motion

Any ideas? Anders On Fri, Oct 13, 2017 at 3:15 PM, Anders Støttrup Larsen wrote: > Hi all > > I have been trying to simulate a system containing two walls and a > slab/vacuum. During the simulation water from the slab diffuses into the > vacuum as intended. The problem is that this causes the s

Re: [gmx-users] new i9 processor

Hi, There's no real issue there. If anything, it's simpler. With the dual socket system it would often make no sense to extend an OpenMP region across the sockets. That's still true if there's internal structure that makes some cores further from others (I dunno if true for Skylake-X). You'd still

Re: [gmx-users] new i9 processor

Dear Harry, we have several nodes with single i9 7900 decacore processors and one gtx 1080ti each. So far they show very good performance compared with dual 16 core xeon nodes with two K20x and even K40x cards. We reach a performance of >40ns per day for >9 atoms with the i9 system, compa

Re: [gmx-users] new i9 processor

Dear Harry, we have several nodes with single i9 7900 decacore processors and one gtx 1080ti each. So far they show very good performance compared with dual 16 core xeon nodes with two K20x and even K40x cards. We reach a performance of >40ns per day for >9 atoms with the i9 system, compa

[gmx-users] Water tracking along simulation

Hello everyone, It is any tool to track water molecules (or a particle in general) along a simulation trajectory, so the final result is the pathway/streamline of selected water molecules? It would something similar to what was done in this paper http://pubs.acs.org/doi/abs/10.1021/bi901900s.

Re: [gmx-users] Regarding Residue in chain has different type (Other) from starting residue

On 10/15/17 11:27 PM, Dilip H N wrote: Thank you Justin Sir, 1] But how do i solve this issue..?? and make sure that pdb2gmx is not interpreting my input as being a single chain and it's finding dissimilar residue types..?? even i tried with gmx pdb2gmx with -ter command, but still, i am getti

Re: [gmx-users] Energy minimization issue

On 10/16/17 5:19 AM, Khadija Amine wrote: Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has stop

Re: [gmx-users] Water tracking along simulation

On 10/16/17 7:16 AM, Yasser Almeida Hernández wrote: Hello everyone, It is any tool to track water molecules (or a particle in general) along a simulation trajectory, so the final result is the pathway/streamline of selected water molecules? It would something similar to what was done in th

[gmx-users] Fw: Two questions about PME-User in coulombtype

Dear Hess, I have two questions about the usage of the PME-User in coulombtype parameter. I didn't get replies from the GMX-USER mail list. Could you please give some details? The forwarded mail is the two questions I asked. Thanks for your help. Yu -Original Messages- From: "Du, Yu"

[gmx-users] possible bug in convert-tpr

Hi All, I think that there is a bug in "gmx convert-tpr", as I understand that "gmx dump" dumps wrong atom types and some wrong numbers when working with some modified tpr files. I attach clear instructions on how to get the bug, as well as two input files and the faulty .trp. I found the pro

Re: [gmx-users] new i9 processor

BS”D Dear Bernard, Thank you for your reply and info. Our experience with a second graphics card (when coupled with the appropriate number of cores) is that we garner close to a 100% performance gain. We have access to nodes on a cluster with 16 cores (2 x E5-2630 v3) + 1 K80 (dual gpu on

Re: [gmx-users] new i9 processor

Dear Harry, you are right for the dual xeon 16 core setup you (and we) use, but for the single core i9 setup we made the experience, that we only gained between 5-10% of performance by adding a second gpu. This was what I was hinting here... Best Bernhard Am 16/10/17 um 14:56 schrieb Harry

[gmx-users] Question about "gmx traj" command

Dear Gromacs Users, I have a question about the gmx traj in order to calculate the force components. I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes It produced "force_all_z_l9.xvg" file. In the file, there are four columns. The first

Re: [gmx-users] Question about "gmx traj" command

On 10/16/17 9:36 AM, Chang Woon Jang wrote: Dear Gromacs Users, I have a question about the gmx traj in order to calculate the force components. I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes It produced "force_all_z_l9.xvg" file

Re: [gmx-users] new i9 processor

On Mon, Oct 16, 2017 at 2:56 PM, Harry Mark Greenblatt wrote: > BS”D > > Dear Bernard, > > Thank you for your reply and info. Our experience with a second graphics > card (when coupled with the appropriate number of cores) is that we garner > close to a 100% performance gain. We have access

[gmx-users] gromacs error

Hi, How can i rectify the following GROMACS error? Fatal error: atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms while sorting atoms. Thank you for your help -- *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des Matériaux à l'état condensé, Lab

Re: [gmx-users] gromacs error

On 10/16/17 12:17 PM, Rahma Dahmani wrote: Hi, How can i rectify the following GROMACS error? Fatal error: atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms while sorting atoms. Either correct the atom names to what the force field expects, or simplify life and use -ign

Re: [gmx-users] grompp error

My guess would be that when you thought ran it with the increased box size coordinate file, you actually used the original coordinate file. FYI http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_eleme

[gmx-users] how to do dPCA?

Dear gromacs users I would like to do dPCA for my 100ns trajectory. When see in the gromacs tutorial I could not create the covar.ndx file. My peptide is 20 residues length. I made .ndx file for dihedral angles and after generating the dangle.trr file. But here I have one problem, to generate the