BSD
Gromacs is telling you that the -h option you supplied is not valid for this
command. You can see all the valid arguments for each
command here
http://manual.gromacs.org/online.html
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
Hi there,
On 23 Dec 2014, at 08:59, Harry Mark Greenblatt
harry.greenbl...@weizmann.ac.il wrote:
BSD
Gromacs is telling you that the -h option you supplied is not valid for this
command.
No, that is not true, the -h option works for all Gromacs commands.
It is exactly this option that
Dear Users,
I am learning free energy calculations using MD (Desolvation free energy of
Methane in water) from Justin Lemkul's tutorials. For this I have installed
gromacs-5.0.1 version on my Mac Pro workstation and proceeding with the
calculations as mentioned in the tutorials. When I ran mdrun
Hello all
Can any one please tell me What is Implicit and explicit solvation??
And Which kind of solvation is used in Justin A. Lemkul tutorial??
With Regards
Neha bharty
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Dear Neha,
Wikipedia (or any simulation textbook) can!
http://en.wikipedia.org/wiki/Implicit_solvation
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
... and see
http://www.gromacs.org/Documentation/Installation_Instructions#portability-aspects
Mark
On Tue, Dec 23, 2014 at 7:25 PM, Carsten Kutzner ckut...@gwdg.de wrote:
Hi there,
On 23 Dec 2014, at 08:59, Harry Mark Greenblatt
harry.greenbl...@weizmann.ac.il wrote:
BSD
Gromacs is
Hi Jinxin,
Better try trjconv -pbc whole
trjconv -pbc nojump should work if your protein is whole (and matching) in
the reference structure.
Fittings screws up the PBC.
Cheers,
Tsjerk
On Dec 23, 2014 6:02 AM, jinxin 18819028...@163.com wrote:
Hi Tsjerkthank you very much ! as you said,
Dear all,
my project involves around the interaction of DNA with small
molecules. I want to calculate (rather show) the native H-bond breaking of
a double stranded DNA in the presence of three ions. Some of my ions are
capable of making secondary H bonds and I want to show that as
Hi all,
I am trying to study wetting of water on Graphene oxide(GO). My
structure has functional group in form of Hydroxyl and epoxide group
on only one side of the Graphene sheet. Also I have added water
molecules in form of spherical droplet on the same side of the sheet.
Since my simulation
Dear Justin A. Lemkul,
I want to use pulling code for calculate the PMF of a molecule at the across
the DMPC, but i can't obtained a large pull across the membrane my pulling code
was:
; Pull code
pull= umbrella
pull_geometry= position
pull_dim= N N Y
pull_start = yes; define
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