[gmx-users] Running MD simulation with Multiple ligands

I need to run a MD simulation with two ligands 01. Natural Substrate (GTP) 02. Allosteric drug candidate bounds closer to the substrate binding pocket. single itp file was created , combining both ligands using Swiss pharm for CHARMM force field. I am unable to continue from the add ion step bec

Re: [gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

Hi, It's only the number of that type of bond, and there are very many types of bond. Note that pairs are handled in their own routine. You should really be modifying newer versions of GROMACS. Doing so off an old released version ensures you benefit from none of the improvements or bug fixes sin

[gmx-users] Calculated bonded interactions - number of bonds- bondfree.c

Hi all, I am trying to look into the source code of Gromacs 5.0.7 to see how Gromacs calculate bonded interactions. For example, to calculate bond interaction between 2 atoms, there is the function (gmxlib/bondfree.c): real bonds(int nbonds, ...) { for (i = 0; (i < nbonds); ) {

[gmx-users] No default Proper Dih. types when using neutral terminal

Hi everyone, I have a list of short peptides generated from PyMOL. I am ignoring all the hydrogen atoms and use neutral terminal caps for both ends. All seems fine from pdb2gmx to solvation. The problem kicks in when I add ions. *Here was what I did - * 1. pdb2gmx 2. editconf 3. solvat

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

On 10/25/17 9:33 AM, Dilip H N wrote: Sir, As u have mentioned in the link http://www.gromacs.org/Documen tation/Terminology/Force_Fields/CHARMM the cutoffs are described here for CHARMM FF. So similarly, how can i get the cutoffs for OPLSAA, Amber, GROMOS etc., forcefields in gromacs..?? Is th

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

Sir, As u have mentioned in the link http://www.gromacs.org/Documen tation/Terminology/Force_Fields/CHARMM the cutoffs are described here for CHARMM FF. So similarly, how can i get the cutoffs for OPLSAA, Amber, GROMOS etc., forcefields in gromacs..?? Is there any source, or only through literature

Re: [gmx-users] CHARMM36 older version (GROMACS)

On 10/25/17 4:11 AM, João Henriques wrote: Hi Simon, Aren't they the same force field though? As far as I've noticed they're identical if you use them for proteins (without any fancy residues). The latest one just includes more atom types, etc. From my understanding the latest one is more "com

Re: [gmx-users] No performance increase with single vs multiple nodes

Hi, On Wed, Oct 25, 2017 at 4:24 AM Matthew W Hanley wrote: > > There's several dozen lines of performance analysis at the end of the log > > > file, which you need to inspect and compare if you want to start to > > understand what is going on :-) > > Thank you for the feedback. Fair warning, I

Re: [gmx-users] CHARMM36 older version (GROMACS)

Hi Simon, Aren't they the same force field though? As far as I've noticed they're identical if you use them for proteins (without any fancy residues). The latest one just includes more atom types, etc. From my understanding the latest one is more "complete", but both are essentially the same thing

[gmx-users] CHARMM36 older version (GROMACS)

Hi everyone, I plan to use CHARMM36-nov2016.ff for my simulation. However, MacKerell Lab webpage does not seem to provide CHARMM36-nov2016. Only CHARMM36-jul2017 is provided. I tried to google "CHARMM36-nov2016" but failed to see any official downl