Re: [gmx-users] friction constant for free energy calculation

On 2/6/19 7:28 AM, minky son wrote: Dear gmx users, I was trying to calculate free energy. I’m confused about setting the appropriate value for friction constant (= 1/tau-t). In gmx manual, a value of 0.5 ps-1 (tau-t = 2.0 ps) was suggested but 1.0 ps-1 (tau-t = 1.0 ps) was used in

[gmx-users] Odd results from rerun for solvent water

Dear Gromacs users, I've encountered an odd problem regarding md -rerun. I'm looking at a small molecule dissolved in water (TIP3P or TIP4P/2005). I've generated the trajectory of the system and used this trajectory to perform a rerun. The .trr seems fine (visualized in VMD, analyzed with

Re: [gmx-users] gmx trjconv -center not working?

Thanks...but these don't really address the issue I have. I've written my own script now to do re-centering and looping of atoms across the box walls myself, but I am still really unclear why -center does not in fact center the molecule in the box either at its geometric center OR its center of

Re: [gmx-users] CHARMM or AMBETR forcefield for methylated glutamine and glutamic acid.

On 2/6/19 9:38 AM, Gyorgy Hantal wrote: Hi, I think you should be able to do that if there are (and I think there should be) corresponding entries in the chramm/amber rtp file. Neither AMBER nor CHARMM has methylated glutamine. If this sounds alien to you, try find out what is the way to

Re: [gmx-users] Distance COM of two systems

On 2/6/19 11:26 AM, Antonio PEÓN wrote: Hello, I would like to calculate the distance from the center of masses (COM) between two systems. One would be the center of mass of waters and another would be the center of mass of a lipid membrane. I was using this command and wanted to know if it

Re: [gmx-users] Total time of ligand in active site

Hi, Sure, count the number of frames where the position of ligand atoms is suitably close to the active site. There are definitely good and bad ways to define that criterion, however. Mark On Thu, 7 Feb 2019 at 10:18 Pandya, Akash wrote: > Hi all, > > I wanted to find out if there was a way

Re: [gmx-users] gmx trjconv -center not working?

Hi Justin, I've verified the I'm entering in the right group and that it's correct in the index file. Where do I find the output for what it thinks is the center of mass before and after? That would be helpful output, but I haven't found such output in standard output or error. thanks again

Re: [gmx-users] gmx trjconv -center not working?

On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote: Hi Justin, I've verified the I'm entering in the right group and that it's correct in the index file. Where do I find the output for what it thinks is the center of mass before and after? That would be helpful output, but I haven't found such

Re: [gmx-users] gmx trjconv -center not working?

On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote: Thanks...but these don't really address the issue I have. I've written my own script now to do re-centering and looping of atoms across the box walls myself, but I am still really unclear why -center does not in fact center the molecule in the

Re: [gmx-users] Ionic conductivity

On 2/6/19 1:08 PM, Jianna Blocchi wrote: Hi thereWhen the ionic conductivity changes during the time!Analysis shows that at different time intervals, the ionic conductivity changes.I divide the production run time to 3 intervals of time. At each of them, I get a different ionic

[gmx-users] Problem about Cgenff lone pairs

Dear all, I would like to run simulation for some small molecules containing Chlorine with CHARMM36 forcefield. I was using cgenff to generate the gromacs topologies. It seems cgenff_charmm2gmx.py script currently cannot convert topologies containing lone pairs. Does anyone know other way to

[gmx-users] ligand-polymer interaction in triclinic unit cell

Hello everyone, I am trying to simulate interaction of polymer with ligand. The polymer is represented by infinite sheet build by propagation in 2 dimensions of monomer obtained from crystal structure. Since the polymer was crystallized in triclinic unit cell, the propagation of the sheet also

[gmx-users] atoms-atoms distance

Dear expertsHow can I calculate distances between special atoms of group A and special atoms of group B?There is a huge number of atoms and making them as pair index is so time consuming and difficult!Thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gmx trjconv -center not working?

Hi Justin, Thank you -- the good news is that the center of mass of this group does in fact match what I calculate to be the COM with my script. BUT, the bad news is that this is not in the center of the box after I have asked for it to be centered (which I presume it should be):: COM: 5.95324

[gmx-users] x2top finds 10+ bonds on atoms

Dear gms users, I’ve been using x2top for some time with success.. I recently taken a polymer whose itp was created with x2top and using the same 55a7 ff and re-ran it as a demo-tutorial. In leaning how to use x2to and atomname2type I expected the error “ Cannot find forcefield for atom

Re: [gmx-users] x2top finds 10+ bonds on atoms

Found the problem, In using the -ff select option, x2top was being directed to an incorrect gromos54a7 .ff directory - not the one in the local directory - with an incorrect n2t. x2top was apparently doing its best to make something. > On Feb 7, 2019, at 7:07 PM, paul buscemi wrote: > >

Re: [gmx-users] Position restrained energy minimization

When you run EM with -v directive, you will see how much is the largest force value applies to your atom. Try to estimate whether that force constant was enough to keep your atom fix because if your structure has any overlap, force can be very large On Thu, Feb 7, 2019 at 6:40 AM Ashraya

[gmx-users] Total time of ligand in active site

Hi all, I wanted to find out if there was a way of calculating the total time a ligand was present in the active site during the MD simulation? Many thanks, Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Position restrained energy minimization

That will still allow peptide atoms to move (if only a little). AFAIK Gromacs is not really fit for rigid body studies, but you can set all bonds and angles to constraints (mdp option: constraints=all-angles). This may or may not work. Torsion angles will still be free to rotate though. From the

[gmx-users] More details on the "Steepest Descents"

Dear Gromacs friends, I am trying to understand more on the "Steepest Descents" so that I can decide if I need to better minimise the system by reducing the "emtol" or increasing the "nsteps", or other ways. The prompt is shown in the end. My understanding is, the algorithm randomly chooses

Re: [gmx-users] offloading PME to GPUs

Hi, thanks for this information. I wonder if PME offload has been implemented for more than one node simulations? I tried the following command for running on two nodes (with 4 ranks each and 4 OpenMP threads) mpirun -np 8 gmx_mpi mdrun -nb gpu -pme gpu -npme 1 -ntomp 4 -dlb yes the log files

Re: [gmx-users] offloading PME to GPUs

Hi, > On 7. Feb 2019, at 15:17, jing liang wrote: > > Hi, > > thanks for this information. I wonder if PME offload has been implemented > for more than one > node simulations? I tried the following command for running on two nodes > (with 4 ranks each > and 4 OpenMP threads) > > mpirun -np 8

Re: [gmx-users] offloading PME to GPUs

Please see the user guide: http://manual.gromacs.org/documentation/2018.5/user-guide/mdrun-performance.html#gpu-accelerated-calculation-of-pme -- Szilárd On Thu, Feb 7, 2019 at 3:18 PM jing liang wrote: > > Hi, > > thanks for this information. I wonder if PME offload has been implemented > for