[gmx-users] QUERY IN GRO FILE

Hi gromacs users, I have a doubt in this command, grompp -f em.mdp -c conf.gro -p topol.top -o em mdrun -v -deffnm em These commands generate em.gro, em.tpr, em.trr, em.log file. There is another command which is mdrun -s em.tpr which generates confout.gro Does em.gro and confout.gro

[gmx-users] terminated abnormally, message of GridMAT-MD tool

Dear Justin, I am using GridMAT-MD tool for analyses of heterogeneous membranes. I generated trajectory.gro only a group which contains a peptide and lipids. I got following Thread 1 terminated abnormally: Illegal division by zero at GridMAT-MD-parallel.pl line 501. What is the meaning of the

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

Hi Justin, I am really sorry for taking your time. I found my mistake. Earlier this error was not there because I was applying my umbrella potential along x axis only which has almost 120 A. Now I am applying umbrella potential along both x and y axes. That is causing the problem as the y axis

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

So if the actual distance is 2.3 nm why does GROMACS measure it as 3.58 nm ? On Wed, Mar 29, 2017 at 11:11 PM, Sajeewa Pemasinghe wrote: > The coordinates of group1 center of mass are 44.466, 23.909,35.035 and > that of group 2 are 67.467,23.994,34.088 as calculated in

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

The coordinates of group1 center of mass are 44.466, 23.909,35.035 and that of group 2 are 67.467,23.994,34.088 as calculated in VMD . So the distance is 23 A . On Wed, Mar 29, 2017 at 11:05 PM, Sajeewa Pemasinghe wrote: > Hi Justin, > > Thank you for the prompt reply. I

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

Hi Justin, Thank you for the prompt reply. I asked a second question correcting the value of 23.0 nm. The distance value is 2.3 nm. On Wed, Mar 29, 2017 at 10:57 PM, Justin Lemkul wrote: > > > On 3/29/17 2:55 PM, Sajeewa Pemasinghe wrote: > >> Hi everyone, >> >> I have run an

Re: [gmx-users] Box dimensions in the gro file are not read by GROMACS

On 3/29/17 2:55 PM, Sajeewa Pemasinghe wrote: Hi everyone, I have run an equilibration of two linear molecules in a water box with dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated structures (not the final structure) in the final nanoseconds as starting structures for an

[gmx-users] Box dimensions in the gro file are not read by GROMACS (correcting an error in the previous question)

Hi everyone, I have run an equilibration of two linear molecules in a water box with dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated structures (not the final structure) in the final nanoseconds as starting structures for an umbrella sampling calculation. The problem is that

[gmx-users] Box dimensions in the gro file are not read by GROMACS

Hi everyone, I have run an equilibration of two linear molecules in a water box with dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated structures (not the final structure) in the final nanoseconds as starting structures for an umbrella sampling calculation. The problem is that

Re: [gmx-users] Format for predefined positions insert-molecules

On 3/29/17 12:52 PM, Svetomir Hitov wrote: Hello, I have been going through the documentation and mailing list for the last couple of days, but I cannot find anywhere, what the format for the predefined insertion trial positions should be. Insert-molecules should use I'd start with the last

Re: [gmx-users] mdrun error

On 3/29/17 11:49 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello, After equilibrating my system for 100 ns( during which there was restraint on the protein letting the lipids to equilibrate), when I am trying to run my unrestrained run I am getting the following errors: 1. "bonds that rotated

Re: [gmx-users] Replica Exchange for surface tension

On 3/29/17 11:29 AM, gozde ergin wrote: Justin what would you suggest if I simulate the system under constant surface tension since I know the correct surface tension from experiments. Can I get some information about the force field quality if I compare the conformation of the surface under

[gmx-users] Format for predefined positions insert-molecules

Hello, I have been going through the documentation and mailing list for the last couple of days, but I cannot find anywhere, what the format for the predefined insertion trial positions should be. Insert-molecules should use that file to place molecules inside the box in certain places. I have

[gmx-users] mdrun error

Hello, After equilibrating my system for 100 ns( during which there was restraint on the protein letting the lipids to equilibrate), when I am trying to run my unrestrained run I am getting the following errors: 1. "bonds that rotated more than 30 degree" 2. "1 particles communicated to PME rank 0

Re: [gmx-users] Replica Exchange for surface tension

Justin what would you suggest if I simulate the system under constant surface tension since I know the correct surface tension from experiments. Can I get some information about the force field quality if I compare the conformation of the surface under constant surface tension (N\gammaT) and

Re: [gmx-users] importance of nvlink in GPU nodes?

thank you very much Mark and Szilard! From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Szilárd Páll Sent: 29 March 2017 10:09:05 To: Discussion list for

Re: [gmx-users] potential energy of a system

Dear Mark and Justin, Thanks a lot for the information On 29 March 2017 at 18:33, Justin Lemkul wrote: > > > On 3/29/17 8:43 AM, Mark Abraham wrote: > >> Hi, >> >> The total potential energy has everything by definition, so I don't know >> what you're asking. >> >> Additivity

Re: [gmx-users] importance of nvlink in GPU nodes?

Note that while, as Mark said, GPU-to-GPU NVLink is not used optimized for, when NVLink is the main CPU-to-GPU interconnect, GROMACS will certainly transfer data across it! Currently only IBM Minsky systems have direct CPU-to-GPU NVLink; on these transfers are ~3x faster than on PCI-E-based

Re: [gmx-users] Replica Exchange for surface tension

Exactly SDS is CHARMM36 but cocobetaine not. > On 29 Mar 2017, at 15:18, Justin Lemkul wrote: > > > > On 3/29/17 9:16 AM, gozde ergin wrote: >> Are you sure it is not CHARMM36 because it is written: >> >> ;; >> ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 >>

Re: [gmx-users] Replica Exchange for surface tension

On 3/29/17 9:16 AM, gozde ergin wrote: Are you sure it is not CHARMM36 because it is written: ;; ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 ;; ;; psf2itp.py ;; ;; Correspondance: ;; j712l...@ku.edu or won...@ku.edu ;; ;; CHARMM36 FF in GROMACS format ;; on the top of the

Re: [gmx-users] Replica Exchange for surface tension

Are you sure it is not CHARMM36 because it is written: ;; ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 ;; ;; psf2itp.py ;; ;; Correspondance: ;; j712l...@ku.edu or won...@ku.edu ;; ;; CHARMM36 FF in GROMACS format ;; on the top of the .itp files. > On 29 Mar 2017, at 15:06,

Re: [gmx-users] potential energy of a system

On 3/29/17 8:43 AM, Mark Abraham wrote: Hi, The total potential energy has everything by definition, so I don't know what you're asking. Additivity of the components of the potential energy is an artefact of the construction of the model physics. While it is true that different physical

Re: [gmx-users] NVE run

Thanks a lot Mark... Kind regards, Neda Rafieiolhosseini Ph.D. Student at Institute for Research in Fundamental Sciences(IPM), School of Nano, Tehran,Iran. - Original Message - From: "Mark Abraham" To: gmx-us...@gromacs.org Sent: Wednesday, March 29, 2017

Re: [gmx-users] importance of nvlink in GPU nodes?

Hi, There's no use made of NVLINK in GROMACS. The 2018 release might make some use of it. Mark On Wed, Mar 29, 2017 at 4:19 AM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear users: > > does anybody know if the presence of either CPU-to-GPU or GPU-to-GPU > nvlink affects the

Re: [gmx-users] potential energy of a system

Hi, The total potential energy has everything by definition, so I don't know what you're asking. Additivity of the components of the potential energy is an artefact of the construction of the model physics. While it is true that different physical phenomena underlie some of the components, the

Re: [gmx-users] NVE run

Hi, There's no way to say. Those numbers would be more indicative of a problem if the system was small, or the simulation was short, but we don't know those (and there are many algorithm settings that contribute). What you really need is to know whether the quality of your observables is degraded

[gmx-users] NVE run

Dear gromax users, I have already run my system under NVE condition with dt=2fs and I found the energy drift about -7000 KJ/mol, then I repeated my simulation with dt=1fs again and I found the drift about -1900 KJ/mol. Is it a reasonable value or should I have a smaller drift? THANKS. --

[gmx-users] potential energy of a system

Dear users, Which terms are included in the total potential energy of a system? Does it have COUL-SR and LJ-SR only, or does it also include the 1-4 terms? Thanks in advance. Regards, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's

Re: [gmx-users] Replica Exchange for surface tension

I used CHARMM GUI Input Generator tool both for SDS and cocobetaine. So basically the reason of not getting correct surface tension is bad parametrisation of force field. Then I should not spend time on simulation the replica exchange. Thanks Justin. > On 28 Mar 2017, at 22:48, Justin Lemkul