[gmx-users] Nonsense timing accounting with OpenCL in Haswell

Greetings! I'm trying to set up gromacs-2019 to use OpenCL with my Intel GPU, integrated in a Haswell processor. The log file says it's detected as Intel(R) HD Graphics Haswell GT2 Desktop, vendor: Intel, device version: OpenCL 1.2 beignet 1.3, stat: compatible I'm running beignet as the OpenCL

[gmx-users] N-Formylmethionine

Hello Everyone, I have a small peptide that begins with a N-formylmethionine and was wondering if anyone here has already generated Charmm36 compatible parameters for this special residue (Or for the N-formyl cap alone). Currently, I'm working on adding the cap to the merged.n.tdb, albeit very

[gmx-users] Fw: Hi

With the help of which analysis in Gromacs, we can calculate the number of atoms typej of a molecule jj which are at a radial distance of 0.5 nm from the atom type k from amolecule kk for 30 picoseconds?Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gr

Re: [gmx-users] radius of gyration and moment of inertia

Solution to what exactly? Both sets have a ~1:3:3 ratio, I'd guess you have two prolate spheroids? and it indicates that yes, they have a similar shape as you stated. Or is the concern the fact that there is ~4x difference between agg1 and agg2 I values? That indicates that agg1 is bigger than a

Re: [gmx-users] Bennet error in FEP-calculations for charged ligands.

As free energies get larger, then the error gets less accurate. So if it is reporting 18.51 +/- 2.95 for one of the intervals, that likely suggest there is very little overlap in that area. A total free energy difference of in -6.12 +/- 3.19 for the transformation indicates that the result is no

[gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file.

Dear All, I have a doubt regarding the ld-seed no and .cpt file. If you repeat a simulation with the same .cpt file but different ld-seed no, my guess I should get the same trajectory running in the serial node (1node+1core ), as because of all the velocities are stored in the .cpt file. I did

Re: [gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?

Hi Gromacs is saying that the BCD residue is not present in gromacs list. You have to create topology for that residue. On Wed 23 Jan, 2019, 6:39 PM Edjan Silva I can not generate topologies for a medium molecule > (beta-cyclodextrin) using the "gmx pdb2gmx". I've tested all the force > fields. >

Re: [gmx-users] Free Energy Change of Dihedral Restraints.

Hi, See https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/topol.top#L24801 which implements https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/grompp.mdp#L291 Mark On Wed, 23 Jan 2019 at 13:14 Drew wrote: > Hi all, > > I'm trying to perform

[gmx-users] Bennet error in FEP-calculations for charged ligands.

Hi all! I encountered an error in my relative free energy calculations and do not know how to fix it. Molecules for which I want to carry out calculations contain a carboxyl group. To validate the protocol, I tried to run the fep-calculations of symmetric molecules for which the change in free ener

Re: [gmx-users] delay at start

Hi, That doesn't sound normal. Please share some log files and inputs if you can. Cheers, -- Szilárd On Tue, Jan 22, 2019 at 5:29 PM Michael Brunsteiner wrote: > hi, > i notice that gromacs, when i start an MD simulation usuallyspends up to a > few minutes using only one (out of several possi

[gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?

I can not generate topologies for a medium molecule (beta-cyclodextrin) using the "gmx pdb2gmx". I've tested all the force fields. how to generate the topology files for beta-cyclodextrin using gmx? --- Program:

[gmx-users] Free Energy Change of Dihedral Restraints.

Hi all, I'm trying to perform a free energy calculation to understand the impact of some dihedral restraints I am using to ensure planarisation of the backbone of some oligomers I am working on. I've previously done a fair few Free Energy of Solvation calculations and I had noticed that there

[gmx-users] discrepancy between system charge when starting simulation from a snapshot from another simulation

Hi all, I am trying to simulate a metalloenzyme protein, containing zinc, in gromacs 5.0.2 using gromos54a7 force field. The protein+zinc system has a net charge of +1, to counter which, I am adding a chloride ion using genion. I have simulated this water+protein+zinc+chloride system for a

Re: [gmx-users] COM

Hi I used index.ndx too...but did not work. Thanks Em qua, 23 de jan de 2019 09:07, Quyen VuVan He means, in your first email, your command is using fix.ndx and HAGD group > is in your index.ndx, have you checked it? > > On Tue, Jan 22, 2019 at 7:54 PM laura O. > wrote: > > > Hi, > > > > I al

Re: [gmx-users] COM

He means, in your first email, your command is using fix.ndx and HAGD group is in your index.ndx, have you checked it? On Tue, Jan 22, 2019 at 7:54 PM laura O. wrote: > Hi, > > I already used index.ndx at the line of code but the error kept the same. I > believe this is not the problem > > Thank

[gmx-users] radius of gyration and moment of inertia

Hi, I am trying to find the moment of inertia of an aggregate. I have used the command gmx gyrate -f test.gro -s test.gro -p yes -mol yes -o out.xvg For two aggregates the the shape is similar but the values are very different for Ix Iy Iz For an aggregate 1 Ix Iy I

Re: [gmx-users] Help with respect to processing protein with FE2+

Dear Justin, I had installed ambertools and followed the tutorial - http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm Currently, I am using gaussian to run the optimization part for obtaining parameters. During the process, I realized that the ligand is not picked up as a residue interac