Re: [gmx-users] new i9 processor

Hi, It's not only the core count that matters, the speed of the cores also does! For that reason, the high-clock Intel i9 and Threadripper CPUs will be often faster than many dual socket machines with more cores. BTW, servethehome.com has recently started doing benchmarks with GROMACS and has

Re: [gmx-users] Regarding ATB/PRODRG server for charmm 36 FF

On 10/17/17 2:03 PM, Dilip H N wrote: Hello, 1] I want to run simulations using charmm 36 FF in gromacs, will it be compatible with charmm 36 FF ..?? 2] How does it asses the molecule naming since in each force field the atoms of the molecules may be named differently... Any suggestions...

[gmx-users] WG: Adding a Mg2+ Dummy model to GROMACS AMBERff03

Hi, I am adding a Mg2+ Dummy model to the AMBERff03 FF in GROMACS 2016.3,using the paramters from Jiang et al. (given in the supporting material) http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00286as the newest and "most reliable for ATP-Mg2+-Protein conformations". I was able to implement

[gmx-users] Regarding ATB/PRODRG server for charmm 36 FF

Hello, 1] I want to run simulations using charmm 36 FF in gromacs, will it be compatible with charmm 36 FF ..?? 2] How does it asses the molecule naming since in each force field the atoms of the molecules may be named differently... Any suggestions... Thank you. -- With Best Regards,

Re: [gmx-users] Errant hydrogen bonds in the Lysozyme tutorial -- Please advise

On Sun, Oct 15, 2017 at 3:13 PM, Deron Johnson wrote: > BTW: I’m using > > gromacs 5.1.4 > VMD 1.9.3 > > on a Macbook Pro with macOS 10.12.3 (Sierra). > > > On Oct 15, 2017, at 12:08 PM, Deron Johnson wrote: > > > > I am new to gromacs. I followed the

Re: [gmx-users] Errant hydrogen bonds in the Lysozyme tutorial -- Please advise

BTW: I’m using gromacs 5.1.4 VMD 1.9.3 on a Macbook Pro with macOS 10.12.3 (Sierra). > On Oct 15, 2017, at 12:08 PM, Deron Johnson wrote: > > I am new to gromacs. I followed the steps of the lysozyme tutorial >

Re: [gmx-users] Creating cyclic peptides

Dear Maud, Thanks, I will give that a try, Regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maud Jusot Sent: 17 October 2017 16:10:42 To:

Re: [gmx-users] Creating cyclic peptides

Dear James, If you want to use an Amber force field, you can create the topology in the amber format with AmberTool and then convert it to the gromacs format using Acpype tool (http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder). It works for cyclic peptides. Best regards, Maud Le

Re: [gmx-users] Creating cyclic peptides

Thanks Justin, Is there anyway of getting it to work using an AMBER forcefield as well? Kind regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul

Re: [gmx-users] Creating cyclic peptides

On 10/17/17 10:13 AM, Easton J.W. wrote: Hi, I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to do this using either an AMBER or CHARMM forcefield. Initially I have been following the instructions in this link,

Re: [gmx-users] Umbrella sampling: issue with COM distance far from initial value

On Tue, Oct 17, 2017 at 8:05 AM, Giuseppe Léonardo Licari < giuseppe.lic...@unige.ch> wrote: > Dear all, > > I have troubles with umbrella sampling. During the umbrella sampling > simulation the COM distance between the two solutes is going too far from > the set initial value. I tried to

[gmx-users] Creating cyclic peptides

Hi, I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to do this using either an AMBER or CHARMM forcefield. Initially I have been following the instructions in this link, https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html

[gmx-users] Umbrella sampling: issue with COM distance far from initial value

Dear all, I have troubles with umbrella sampling. During the umbrella sampling simulation the COM distance between the two solutes is going too far from the set initial value. I tried to increase a lot the force constant of the harmonic potential. I also tried to change "umbrella" to

[gmx-users] (no subject)

Hi all, I have a very basic question about essential dynamics. I want to know whether essential dynamics function is similar to Accelerated MD ? Or essential dynamics is different from Accelerated MD ? Thanks in advance. Kingsleg Theras -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] new i9 processor

BS”D On 17 Oct 2017, at 1:03 PM, Bernhard Reuter > wrote: Dear Harry, I would assume you are right with your argument that 6/8/10 cores per GPU are better than i.e. 5 cores. If I were you I would still carefully test, if you really have

Re: [gmx-users] Gromacs 5.1.4

Hi, CUDA 9.0 doesn't support that ancient architecture, but old GROMACS code didn't know that would happen. Either use an older CUDA or a newer GROMACS, e.g. 2016.4. Mark On Tue, Oct 17, 2017 at 11:34 AM Chetan Puri wrote: > I am trying to install Gromacs 5.1.4 on

Re: [gmx-users] new i9 processor

Dear Harry, I would assume you are right with your argument that 6/8/10 cores per GPU are better than i.e. 5 cores. If I were you I would still carefully test, if you really have a big performance gain with a i9 16 core and two vs. one GPU. There are two reasons for this: 1. The 1080ti is

[gmx-users] Gromacs 5.1.4

I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40 But on the make step I am getting error nvcc fatal : unsupported gpu architecture 'compute_20' So can anyone suggest how to resolve it. CHETAN -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] new i9 processor

BS”D Dear Bernhard and Szilárd, Since your replies to me are related, I’ll combine my replies to one letter. 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

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

Hi, Force is a vector, yes. And its units are not kcal/mol nm in GROMACS. See chapter 2 of the reference manual. Mark On Tue, Oct 17, 2017 at 9:00 AM Chang Woon Jang wrote: > Dear Justin, > > Thank you for your help. One more question is that there are positive >

Re: [gmx-users] Running MD simulations at a particular temperature

Hi, That's your question as part of your experimental design. Why do you want to do simulated annealing? Mark On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash wrote: > Is simulated annealing carried out during NPT or in the production run? > > Akash > > -Original

Re: [gmx-users] Running MD simulations at a particular temperature

Is simulated annealing carried out during NPT or in the production run? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 20 September 2017 03:20 To:

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

Dear Justin, Thank you for your help. One more question is that there are positive and negative values. Does this mean that the forces are written as vector values? For example, the value of -40 means negative Z direction with 40 kcal/mol nm ? Thank you. Best regards, Changwoon Jang On