hello gromacs users
thanks justin i have applied
perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
mdrun -v -deffnm em
perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
after that solvation step but no command is present in dppc tutorial should
i
Hi Abhijit,
Following is my mdp file:
; VARIOUS PREPROCESSING OPTIONS
title=
cpp= /lib/cpp
include =
define = -DFLEXIBLE
; RUN CONTROL PARAMETERS
integrator = l_bfgs
; Start time and timestep in ps
tinit
Dear Manu Vajpai,
On 07 Jul 2014, at 07:39, Manu Vajpai manuvaj...@gmail.com wrote:
Hi all,
I am interested in using accelerated MD or another method which allows me
to sample rare events without specifying collective variables beforehand.
The only solution that I have found for GROMACS so
hello everyone
after this step now i am in the
grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
step but after running i got error
Fatal error:
number of coordinates in coordinate file (solv.gro, 101917) does not match
topology (topol.top, 604599)
i have been edited the sol (counted from
hello gromacs users
i am applying (solv.gro 101917-108573 topol.top )/3
= i have to subtract 2218.66 into old figure (32672 which is present in
topol.top )
due to float no still error persist only one coordinate is different
Fatal error:
number of coordinates in coordinate file (solv.gro,
hello gmx users
i am also getting that error
[file topol.top, line 24832]:
System has non-zero total charge: 14.788998
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer
On
On 7/7/14, 12:49 AM, Andy Chao wrote:
Dear GROMACS Users:
I have a question regarding using the GROMPP command..
I first used the g_x2top command to convert the *.gro file of a graphene
sheet to the *.top file of the graphene sheet by using the forcefield.itp
file in the OPLSAA file folder
hello
the command is gmx grompp when i am running
gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
No command 'gmx' found, did you mean:
Command 'gm' from package 'graphicsmagick' (universe)
Command 'pmx' from package 'pmx' (universe)
Command 'ngmx' from package 'gromacs'
On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote:
Hi all,
After getting the topology file for graphene, when i tried to freeze graphene
and do energy minimization with just water molecules around it, then the
graphene structure becomes distorted ie. the upper layer of the graphene
shifts down and
On 7/7/14, 2:35 AM, RINU KHATTRI wrote:
hello gromacs users
thanks justin i have applied
perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
mdrun -v -deffnm em
perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
after that solvation step but no
BSD
Dear All,
I was given access to a test machine with
2 x E5-2630 2.3GHz 6 core processors
2 x Tesla K20x GPU's
Gromacs 5.0, compiled (gcc 4.4.7) with support for Intel MPI.
Ran a 1ns simulation on a 3-domain (all in one chain) DNA binding protein,
dsDNA, waters, and ions (~32,600 atoms).
BSD
Dear All,
I was given access to a test machine with
2 x E5-2630 2.3GHz 6 core processors
2 x Tesla K20x GPU's
Gromacs 5.0, compiled (gcc 4.4.7) with support for Intel MPI.
Ran a 1ns simulation on a 3-domain (all in one chain) DNA binding protein,
dsDNA, waters, and ions (~32,600 atoms).
On 7/7/14, 6:34 AM, RINU KHATTRI wrote:
hello
the command is gmx grompp when i am running
gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
No command 'gmx' found, did you mean:
Command 'gm' from package 'graphicsmagick' (universe)
Command 'pmx' from package 'pmx' (universe)
Hi Justin,
Thanks for the reply. Actually I am having the problem of z- dimension to be
zero only when I am giving pbc only in xy direction. For pbc in xyz, the z
dimension is not becoming zero. So do you still think it can be because of
improper box size chosen?
Also I have not given nwall
Dear all,
I am studying a water-methane system with tip4p-Ice for water and
oplsaa for methane.
What I want to try is modify the intermolecular non-bonded interaction
between methane and water. I just want to multiply the combination rule
(geometric mean) used to obtain the mean well depth
Hi List,
I have simulated peptides in explicit water to form aggregate. I tried
various options to post-process my trajectory (after removing water) using
Gromacs 4.6.3 as described below. I want to record movie using VMD but the
molecule translates and rotates during movie hence, I cannot
Hi
I am trying to run an md simulation. after using mdrun the failure message
was: illegal instruction, core dumped
I have used ulimit -c unlimited but my problem is not solved.Could you
please help me?
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Gromacs Users mailing list
* Please search the archive at
Dear all,
I have trouble creating a FF without bonds explicitely defined,
only using nonbonding forces of the Buckingham (BH) type to keep
my crystal in one piece. The problem is related to wrong interatomic
forces on basis of the ASCII-dumped TRR files. So FF works (at
least functionally),
Hi GROMACS users,
GROMACS 4.6.6 is officially released. It contains many bug fixes, including
significant fixes to non-bonded interactions that use modifiers, of
particular importance in free-energy calculations. We encourage all users
to upgrade their installations from earlier 4.6.x releases.
Hi Erik
Thanks for your hints
Sorry, I have problems with internet, so I could not answer you before
I thought something was wrong with the MD simulation at physiological solution
since it looks like as a MD simulation at water. But I did not take into
account the protonation states!!!
Hi Chris,
I'm not sure if this is what you need specifically but I've been
looking at protein denaturation in acidic and alkaline medium and the
strategy that I've come up with is to generate a pdb file with the correct
protonation state using this online tool
On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote:
Hi Justin,
Thanks for the reply. Actually I am having the problem of z- dimension to be
zero only when I am giving pbc only in xy direction. For pbc in xyz, the z
dimension is not becoming zero. So do you still think it can be because of
improper box
On 7/7/14, 8:36 AM, sujithkakkat . wrote:
Dear all,
I am studying a water-methane system with tip4p-Ice for water and
oplsaa for methane.
What I want to try is modify the intermolecular non-bonded interaction
between methane and water. I just want to multiply the combination rule
On 7/7/14, 8:47 AM, abbas yousefpour wrote:
Hi
I am trying to run an md simulation. after using mdrun the failure message
was: illegal instruction, core dumped
I have used ulimit -c unlimited but my problem is not solved.Could you
please help me?
You've compiled mdrun with a level of
Dear GMX-users,
I would like to share some scripts which help to automate MD and free energy
calculations with Gromacs. They are written in Bash and thus can be easily
customized for one's specific needs. At present everything is designed to run
absolute solvation free energy calculations of
Dear All,
I recently made a molecular dynamics run of TiO2-water-sodium-formate
system of 12740 atoms. Then I extracted dump file from xtc file of
production run ( NPT, 300 K, 1 bar) using gmxdump command. THere are total
10001 frames. Now, I have found that some quote ( not error/warning) is
On 7/7/14, 6:28 PM, Chetan Mahajan wrote:
Dear All,
I recently made a molecular dynamics run of TiO2-water-sodium-formate
system of 12740 atoms. Then I extracted dump file from xtc file of
production run ( NPT, 300 K, 1 bar) using gmxdump command. THere are total
10001 frames. Now, I have
Thanks, Justin and Roland. While 2/dev/null/ at the end of gmxdump command
removes that quote nicely, adding either of following commands fails. I am
using gromacs 4.6.5.:
Following did not work ( why? curious since above 2/dev/null/ will
suppress all errors getting displayed)
1. GMX_NO_QUOTES =
Hi Justin,
Thanks a lot for your replies. I want to simulate a half cell with graphene
electrode only on one side, hence i am using pbc in only xy direction i.e.
direction of graphene sheet, so that I have a infinite size graphene sheet with
no side effects. But if I use 3D pbc then graphene
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