Re: [gmx-users] simulation a box of water

Thank you Justin I don't understand. Do I use the explicit water molecules or the model? and where do I used the "define = -DFLEXIBLE" option? please explain a bit more! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Yep thanks you are right! It seems that lacking of the FG topology is real problem here. Does the |Reverse transformation| method also require the same input data for back to FG representation including innitial FG topology7 Thanks in advance! J. 2016-03-17 17:20 GMT+01:00 : > Hi James, > From

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

so should i go for sol molecules :1612 Na :11 On 17 March 2016 at 21:44, Peter Stern wrote: > Missing atoms in GLU 474 is because the coordinates for the GLU side chain > weren't resolved in the crystallographic data and aren't included in the > pdb file. Long bonds are

[gmx-users] atomtypes vs atomtypes.atp

Dear all: I never used atomtypes.atp file, rather i always use [atomtypes] directive to provide MW, epsilon, sigma. Is it a problem not to use atomtypes.atp file? --Masrul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b

[gmx-users] Custom forcefield tutorial?

Hello, I would like to perform some simulations with my own simple forcefield. Just a chain of beads, with Lenard-Jones, some harmonic and angle potential, and play with it's parameters. I don't want to write all the computing part from the scratch. I rather to use Gromacs (if it is possible?),

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Hi James, There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to reconstruct the atomistic structure from a CG structure. Here is the respective tutorial  http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward  (from the MARTINI group), and here is the paper of th

Re: [gmx-users] Re :Using FFTK generated parameter file for Protein-Ligand simulations

Dear Justin, I have used CGenFF for CHARMM. However, I am not able to understand how to include the topology of inhibitor to start a simulation. The metal ions which I had talked about are FL and BR and I have got their parameters already from CHARMM. I am relatively new to gromacs, I just wanted

[gmx-users] Inconsistent behavior for bonds involving dummy atoms for alchemical perturbation

Dear GROMACS users, I've been attempting to calculate delta G values for GXG tripeptide mutations as a test case to validate and benchmark my set up, but I have run into a host of issues and curiosities, one of which I describe below. Depending on the direction in which I carry out a mutation, a

[gmx-users] Hydrogen bonding pair selection

Dear Gromacs Users, I was trying to calculate the number of hydrogen bonds between the “O” on Proline (acceptor) and the “N-H” on Glycine (donor) in my system. There are 16 Proline residues and 32 Glycine residues. I first used command “make_ndx" to create two groups, PRO_&_O and N_H_&GLY, c

Re: [gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

On 3/16/16 3:02 PM, Poncho Arvayo Zatarain wrote: Hello, due to one of my last question and about the error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. How can do large the box? My .g

Re: [gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

I think you should increase your system size, i mean number of atoms or decrease the cutoff length. *.gro file dimension change will not help you, because after equilibration, system will retain it's correct dimension. --Masrul On Wed, Mar 16, 2016 at 2:02 PM, Poncho Arvayo Zatarain < poncho_8...

Re: [gmx-users] Re :Using FFTK generated parameter file for Protein-Ligand simulations

On 3/18/16 6:52 PM, Soumya Lipsa Rath wrote: Dear Justin, I have used CGenFF for CHARMM. However, I am not able to understand how to include the topology of inhibitor to start a simulation. The metal ions which I had talked about are FL and BR and I have got their parameters already from CHAR

Re: [gmx-users] atomtypes vs atomtypes.atp

On 3/18/16 8:42 PM, Parvez Mh wrote: Dear all: I never used atomtypes.atp file, rather i always use [atomtypes] directive to provide MW, epsilon, sigma. Is it a problem not to use atomtypes.atp file? The contents of atomtypes.atp and the contents of [atomtypes] found in ffnonbonded.itp (or