[gmx-users] high load imbalance in GMX5.1 using MARTINI FF

Hi, I am running some coarse grained simulations of a membrane-protein system using Martini force field. If I ran it using GMX5.1 and the mdp file provided by Martini website for GMX5, the load imbalance will gradually increase to over 80% from 4-10% at the beginning in a few hours. When I

[gmx-users] force/time application for pull

Dear all, Can anyone shed some light as ,Is it possible to apply force/time for pulling in gromacs. Means I want to pull my system in step wise . eg. 0 - t1 force applied f1 t1+dt to t2 force f2 t2+dt to t3 force f3 . . . tn-1 +dt to tn force fn Is it possible.

[gmx-users] Question about relation among couple-moltype , couple-lambda0 and couple-lambda1 parameter in free energy calculation.

Hello, Thank you for your reading.I am trying free energy calculation about base pair mutation(G * T -> G_enol * T). Actually, I explicitly mention a both state A and B in topology file(Atom type, charge, any parameter related). So, I didn't use couple-moltype option because

[gmx-users] make_ndx

Dear all,I need to use make_ndx, but it doesn't work. I mean, I will put my group numbers, and it finishes successfully, but at the end there is nothing in the .ndx file.  0 System              : 24552 atoms  1 Other               :    576 atoms  2 ACC                 :   504 atoms  3 K+         

Re: [gmx-users] high load imbalance in GMX5.1 using MARTINI FF

Linda, This should indeed normally not happen, but before diving deep into the issue I'd suggest testing more recent releases of GROMACS, preferably 2018.2 so we know if there is an issue in the currently actively supported release. Secondly, load imbalance is not necessarily a bad thing if it

Re: [gmx-users] Errors while trying to install GROMACS-2018

Hi, This is likely an issue with the combination of gcc and CUDA versions you are using. What are these versions? Can you install the latest CUDA (or at least recent) and see if it solves the issue? Cheers, -- Szilárd On Wed, Aug 8, 2018 at 8:00 PM Lovuit CHEN wrote: > Hi everyone, > > > I

Re: [gmx-users] force/time application for pull

On 8/9/18 6:37 AM, Rakesh Mishra wrote: Dear all, Can anyone shed some light as ,Is it possible to apply force/time for pulling in gromacs. Means I want to pull my system in step wise . eg. 0 - t1 force applied f1 t1+dt to t2 force f2 t2+dt to t3 force f3 . .

Re: [gmx-users] Structure of polyvinyltoluene

Genevieve, Create a 3, 4 or 5 mer of the PVT and submit to ATB ( the wonderful topology makers ) to obtain the itp. ( 4A7 ff ) That wil give you the beginning middle and end mers for buiding a plymers as Justin has shown for PE. A second route is to build PVT under 500 atoms and submit

[gmx-users] Protein-Ligand in bilayer

Hi users. It look so complicated to carry out a protein ligand simulation in Lipid bilayer system using charmm ff. I have a ligand with 27 atoms ( includes Hydrogen ). The initial structure (monomer) is simulated in popc constructed using charmm gui web page. To construct the same for the

[gmx-users] Structure of polyvinyltoluene

UNRESTRICTED / ILLIMITÉE Hello! As part of my research, I need the structure of polyvinyltoluene to perform molecular dynamics simulations. I searched for it in Crystallography Open Database (COD) and in Cambridge Crystallographic Data Centre (CCDC), but found nothing. I'm wondering if

Re: [gmx-users] Protein-Ligand in bilayer

Hi, > It look so complicated to carry out a protein ligand simulation in Lipid > bilayer system using charmm ff. I have a ligand with 27 atoms ( includes > Hydrogen ). The initial structure (monomer) is simulated in popc > constructed using charmm gui web page. To construct the same for the >

Re: [gmx-users] Protein-Ligand in bilayer

Hi. Thank you. But the system (protein ligand) is being constructed in charm gui input generator, where it automatically compare the complex pdb and ligand mol2 file ( which will Ben uploaded ). On Thu, 9 Aug 2018 at 11:24 PM, Abhishek Acharya wrote: > Hi, > > > > > It look so complicated to

[gmx-users] Center to center distance in cylindrical micelles

Dear Gromacs Users, I want to calculate the center to center distance of two cylindrical micelles in my simulation. What gmx command should I use to calculate the distance? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at