Hi all,
I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun
command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4.
Can I use the same command line as before for mdrun or other tools?
Thank you very much,
--
J.
--
gmx-users mailing list
Dear all,
I need to add 100 molecules of a second solvent to my polymer. I do this in
two solvation steps as below:
genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500
genbox -cp solute-solvent1.gro -ci Solvent2.gro -o solute-solvent1-solvent2.gro
-nmol 100
1- Is this the
12.01100 ; alkene C (H2-C=)
opls_1441.00800 ; alkene H (H-C=)*
Did I select the correct atomtypes?
Thanks many times!
On 4 April 2013 18:23, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 6:17 PM, Juliette N. wrote:
Hi Justin,
Thanks a lot for your message. I am petrified why
Dear all,
I am having trouble creating topology file for simple molecule ethylene.
Here is the steps. Below is the pdb file:
Ethylene.pdb:
ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00
C
ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00
C
ATOM 3 H11
if you
could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
doubt)?
Do i have to edit esiduetypes.dat?
Thank you many times for your precious time,
On 4 April 2013 17:21, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 11:38 AM, Juliette N. wrote:
Dear all,
I am having
Hi all,
I am trying to produce gro file from PDB file using editconf.
Here is the pdb file
HETATM1 C 0.672 -0.000
0.000 C
HETATM2 C -0.672 -0.000
0.000 C
HETATM3 H 1.238 -0.928
-0.928 0.000
H
1Eth4 H 1.238 0.928 0.000
H
1Eth5 H -1.238 -0.928 0.000
H
1Eth6 H -1.238 0.928 0.000
H
Thanks
On 1 April 2013 20:06, Justin Lemkul jalem...@vt.edu wrote:
On 4/1/13 7:22 PM, Juliette N. wrote:
Hi
Dear gmx users,
Does anyone know how to obtain structure file for the simple ethylene
molecule ( C-C) ? I tried PRODRG but it fails to generate structure files
for di atomic molecules.
Any suggestion is appreciated!
--
Thanks,
J. N.
--
gmx-users mailing listgmx-users@gromacs.org
Hi everyone,
I am trying to calculate error of total energy in edr file using -nbmin
-nbmax options. -nbmax 5 is giving 3% error while -nbmax 3000 gives an
error of 0.91. Can one arbitrarily pick a large -nbmax to obtain less error?
g_energy -f*.edr -nmol X -b XXX -o -nbmin 5 -nbmax 5
Energy
the mean, then something like bootstrapping
may be in order. Information on both of these is readily available on the
web (now that you have a few keywords to search for).
Cheers,
Matt Zwier
On Thu, Feb 21, 2013 at 2:09 AM, Juliette N. joojoojo...@gmail.com
wrote:
Hi everyone,
Does
Hi everyone,
Can anyone advise me on any g_XXX tool in gromacs which can be used to
extract useful information on thermodynamic, surface or structural
properties of polymer chains in solvent other than the properties below?
RDF, Rg. End-to-end distance, structure factor
Appreciate your
Dear all,
I am trying to calculate structure factor or scattering density of a
polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n
index
I provide an index file with System, Polymer (atom numbers of all polymers)
and Solvent (all solvent molecules) groups.
-startq
Hello all,
I am trying to compare PME and shift electrostatics methods for my
hydrocarbon system. In both cases rlist = 1.35 , but in case
of PME rcoulomb= 1.35 while for shift **
rcoulomb= 1.1. I see no significant change (less than 1%) in
total system
Hello all,
I am trying to compare PME and shift electrostatics methods for my
hydrocarbon system. In both cases rlist = 1.35 , but in case
of PME rcoulomb= 1.35 while for shift **
rcoulomb= 1.1. I see no significant change (less than 1%) in
total system
Thanks..You are right...The last line of gro file says 250 so it is in nm!...
On 10 October 2012 12:30, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Sounds like you ran out of memory. Many clusters have a few large-memory
nodes. Can you use one of those?
It's failing on a call for
Hi again,
The reason I have this big box is that I have fully extended chains of
the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
I can fit the chain in the box; and I am going to fill this box with
solvent and use NPT to increase the density. So I dont need to fill up
the
, just an idea.
For the overall system setup, I would rather follow the previous
comments anyway.
On Wed, Oct 10, 2012 at 10:49 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
On Wed, Oct 10, 2012 at 10:24 PM, Juliette N. joojoojo...@gmail.com
wrote:
Hi again,
The reason I have this big
Hello all,
I am going to restart my crashed simulations, but I am not sure which
of *_prev.cpt or *.cpt to use as they contain different written
frames.
*_prev.cpt Last frame -1 time 7462.900
*.cptLast frame -1 time 7468.965
Also on the gmx site it is stated
).)
Good luck,
Matthias
Am 13.08.2012 21:07, schrieb Juliette N.:
Hello all,
I am going to restart my crashed simulations, but I am not sure which
of *_prev.cpt or *.cpt to use as they contain different written
frames.
*_prev.cpt Last frame -1 time 7462.900
*.cpt
...
Any ideas..
Thanks
On 13 August 2012 15:51, Matthias Ernst matthias.ern...@student.kit.edu wrote:
Am 13.08.2012 21:42, schrieb Juliette N.:
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
I see a md_prev.cpt. If I presume correctly
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
mdrun -deffnm md -s -o -c -g -e -x -cpi output
Thanks!
On 13 August 2012 16:10, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:08 PM, Juliette N. wrote:
Yes
, Juliette N. wrote:
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
No, you don't. All you should need (provided the .cpt file is valid, which
it appears to be from the gmxcheck output from before) is:
mpirun -np 8 mdrun_mpi
Thanks, maybe I should re start ... :(
On 13 August 2012 16:36, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:34 PM, Juliette N. wrote:
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened
Velocities 1
Forces 0
Box 1
Is this a valid cpt file?
Thank you,
On 13 August 2012 16:36, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:34 PM, Juliette N. wrote:
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append
All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...
Thank you,
On 13 August 2012 17:04, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:54 PM, Juliette N. wrote:
Hi all,
My cpt file doesnt contain any information?!!
Sure
On 17 May 2012 05:10, Erik Marklund er...@xray.bmc.uu.se wrote:
17 maj 2012 kl. 05.00 skrev Juliette N.:
Hello everyone,
I am trying to estimate the thermodynamic expression, dP/dw at
constant V and T, for my polymer-solvent system. Where P is the
pressure, w is the mass fraction, V volume
Hello everyone,
I am trying to estimate the thermodynamic expression, dP/dw at
constant V and T, for my polymer-solvent system. Where P is the
pressure, w is the mass fraction, V volume and T temperature. I guess
this task can not be done by MD, as for constant Volume, pressure is
meaningless.
/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 101 bonded neighbours molecule type 'Polymer'
Can anyone help me please?
Thanks
On 8 April 2012 17:16, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
On 1 April 2012
April 2012 20:58, Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/04/2012 10:44 AM, Juliette N. wrote:
Hello all,
I am trying to exclude a nonbonded interactions on the polymer chains
using
grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr
and mdrun -rerun command. but when I
On 1 April 2012 20:17, Mark Abraham mark.abra...@anu.edu.au wrote:
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option. mdrun
-rerun should break the total
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option.
mdrun -rerun should break the total nonbonded energy coming from nonboded
energy of (different molecules + a molecule with itself). By setting
On 1 April 2012 20:17, Mark Abraham mark.abra...@anu.edu.au wrote:
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option. mdrun
-rerun should break the total
Thanks. One last question. So whats the new trr file provided by -o
flag of mdrun rerun below?
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
On 1 April 2012 20:17, Mark Abrahammark.abra...@anu.edu.au wrote:
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I
On 1 April 2012 22:07, Mark Abraham mark.abra...@anu.edu.au wrote:
On 2/04/2012 12:05 PM, Juliette N. wrote:
Thanks. One last question. So whats the new trr file provided by -o
flag of mdrun rerun below?
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
If it even
Hi all,
Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt?
Best,
-- Forwarded message --
From: Juliette N. joojoojo...@gmail.com
Date: 1 April 2012 22:10
Subject: Re: [gmx-users] mdrun -rerun
To: Discussion list for GROMACS users gmx-users@gromacs.org
On 1
Hello all,
I read the online instruction on how to extend a run. I just wanted to
double check the procedure because of the NOTE below after issuing
tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 1
NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.
:21, Mark Abraham mark.abra...@anu.edu.au wrote:
On 1/03/2012 5:07 PM, Juliette N. wrote:
Hi all,
Can anyone guide me how one can obtain dihedral distributions of a
polymer chain and how this can be used to ensure the equilibration of
system?
g_angle takes a list of dihedrals and provides
Hi all,
Can anyone guide me how one can obtain dihedral distributions of a polymer
chain and how this can be used to ensure the equilibration of system?
g_angle takes a list of dihedrals and provides the dihedral distribution of
a given dihedral in the time interval -b to -e ?
--
Thanks,
J.
--
On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au wrote:
On 24/02/12, *Juliette N. *joojoojo...@gmail.com wrote:
On 23 February 2012 20:07, Mark Abraham mark.abra...@anu.edu.au wrote:
On 24/02/2012 10:55 AM, Juliette N. wrote:
Hi all,
My average size is 2.9 nm obtained
On 24 February 2012 16:52, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au mailto:
mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote:
On 24/02/12, *Juliette N. *joojoojo...@gmail.com
mailto:joojoojo
Hi all,
My average size is 2.9 nm obtained from NPT under large pressure and now I
intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about
violating minimum image convention.
1- My question is which of rc or rlist is important for minimum image
convention? If its rlist then I
On 23 February 2012 20:07, Mark Abraham mark.abra...@anu.edu.au wrote:
On 24/02/2012 10:55 AM, Juliette N. wrote:
Hi all,
My average size is 2.9 nm obtained from NPT under large pressure and now I
intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about
violating
Hi,
I am trying to figure out the best setting for cut offs and r_switch for my
system based on shift functions.
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 1
rvdw-switch = 1
; Cut-offs
rlist = 1.35
rcoulomb
/2012 2:01 AM, Juliette N. wrote:
Hi,
I am trying to figure out the best setting for cut offs and r_switch for
my system based on shift functions.
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 1
rvdw-switch = 1
; Cut-offs
Hi all,
I am trying to run simulation in vaccum using the the changes shown below
to the usual mdp file.
pbc = no
;coulombtype = PME
;vdw-type= Shift
;Cut-offs
rlist = 0
rcoulomb = 0
rvdw = 0
nstlist =
On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/02/2012 12:22 PM, Justin A. Lemkul wrote:
Juliette N. wrote:
Hi all,
I am trying to run simulation in vaccum using the the changes shown
below to the usual mdp file.
pbc = no
;coulombtype
On 15 February 2012 23:05, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/02/2012 2:08 PM, Juliette N. wrote:
On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/02/2012 12:22 PM, Justin A. Lemkul wrote:
Juliette N. wrote:
Hi all,
I am trying to run
Thanks. That was a new thing for me to learn.
On 15 February 2012 23:19, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/02/2012 3:14 PM, Juliette N. wrote:
On 15 February 2012 23:05, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/02/2012 2:08 PM, Juliette N. wrote:
On 15
Hi all,
I have two simple question on in vacu calculations.
1- Say we start from rc=1, and go all the way to rc=0.1 then we say cut off
has been reduced from 1 nm to 0.1 nm meaning that atoms fall within 0.1 nm
interact with each other. Now when we set rc=0, why dont we consider this
as zero
On 13 February 2012 20:20, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/02/2012 6:26 AM, Juliette N. wrote:
Hi all,
I have two simple question on in vacu calculations.
1- Say we start from rc=1, and go all the way to rc=0.1 then we say cut
off has been reduced from 1 nm to 0.1 nm
Dear all,
Has anyone here have idea on how one can compute heat of mixing for a
binary mixture? Thank you. :)
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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
Dear all,
Can anyone guide me how to access the source code for calculation of
structure factor? I am looking into the scripts directory but cant find
it.
Thanks,
J.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
Hello all,
I am just wondering if analysis tools like g_rdf..can be run in parallel
like mdrun? I have a big system and analysis tools take a lot of time to
finish.
Thanks,
J.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
Dear all,
I am trying to calculate structure factor or scattering density of a
polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n
index
I provide an index file with System, Polymer (atoms numbers of all
polymers) and Solvent (all solvent molecules) groups.
-startq
Dear all,
I am low on disk space and need to delete trr files. I turned on -x option
in all runs so generated xtc files as well. Just wondering if xtc files
contain less information than trr ones which make xtc have less size. Am I
going to lose any information other than velocities?
Thanks,
J.
Dear experts,
I have a quick and naive inquiry. I see in the molecular dynamics
simulations that density of the polymers increase slightly with increasing
degree of polymerization ( or Mw). Even for the systems having the same
total atom numbers but one with less number of chains of higher Mw. My
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure out
when we are referring to equilibration which of the run time or n_steps
parameters are important. One could run 1,000,000 steps with dt of 0.001 ps
or
Hello,
I am trying to extend a simulation to 2 ns and wanted to know if I am using
the proper tools for this purpose. (version 4.5.4)
1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000
mdrun -s old-extend.tpr -cpi old.cpt -o old-extend -c old-extend
-e old-extend
Is
On 10 September 2011 18:03, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
Hello,
I am trying to extend a simulation to 2 ns and wanted to know if I am
using the proper tools for this purpose. (version 4.5.4)
1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr
Dear users,
I have a short question about temperature dependence of enregy terms i.e
bonds, angles, torsions, vdw , electorstatics. I am curious why these
energies increase with T. Especially bonded terms that have no temperature
dependence in the functional form ( force constants), why all
On 6 September 2011 15:03, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
Dear users,
I have a short question about temperature dependence of enregy terms i.e
bonds, angles, torsions, vdw , electorstatics. I am curious why these
energies increase with T. Especially bonded
On 6 September 2011 15:42, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote:
Hello Juliette:
If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.
The larger is a time-step, the larger is a deviation from the energy
Hello everyone,
I know the following question has been discussed many times in the archive
but unfortunately I am still unclear about it therefore I would like to ask
for your patience.
I am interested in non bonded interactions, i.e LJ(SR) and it has been said
that LJ-14 potentials are
On 26 August 2011 12:06, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
Hello everyone,
I know the following question has been discussed many times in the archive
but unfortunately I am still unclear about it therefore I would like to ask
for your patience.
I am interested
On 26 August 2011 13:25, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote:
. Now it is clear that
the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials.
Thank
you so much.
The answer actually depends on what you call nonbonded potential. If
you want to calculate e.g. the
On 26 August 2011 15:17, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
On 26 August 2011 13:25, Dr. Vitaly V. Chaban vvcha...@gmail.commailto:
vvcha...@gmail.com wrote:
. Now it is clear that
the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded
potentials
Dear all,
Sorry if my question sounds irrelevant but I am wondering to know if in
gromacs there is any tool for studying properties like sound wave/acoustic
wave (An acoustic wave is a pressure oscillation that travels through
liquid, in a wave pattern)?
I dont see such a tool in the manual but
Hello,
I set zero charges to all atoms using the commands below:
grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr
tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq
mdrun -s *-ZERO_md -o -c -e -x -v
So before doing mdrun md I add tpbconv command and use the out put
*-ZERO_md.tpr
for the mdrun md
Hi again,
I am wondering if using tpbconv to set zero charges (case 1) works similar
to when one sets zero atom charges in topology file from the very beginning
(case 2). Do these two cases work similarly?
I checked tpr file and I see that charges are set to zero.
Can you please tell me what
July 2011 14:53, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
Hi again,
I am wondering if using tpbconv to set zero charges (case 1) works similar
to when one sets zero atom charges in topology file from the very beginning
(case 2). Do these two cases work similarly
A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
Hello Justin,
I am using tpbconv to set zero charges after em and after doing grompp_md.
grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr
tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq
mdrun -s *-ZERO_md -o -c -e -x -v
Do I need to use
Dear gmx users,
I have two short questions about generation of initial velocities in
simulations. If I want to run simulations at for example 400 K do I have to
alter the temperature for maxwell distribution settings? ( I mean
gen_temp= 400? )
gen_vel = yes
gen_temp
Hello Dear all,
I have a few short questions about pressure coupling settings, namely
isothermal compressibility. I hope you can guide me.
A) By default gmx is taking the value for water but I was wondering if this
has to be modified for other systems.
B) This quantity varies with T and P. so
Hello,
I have a quick question about g_energy output. Can anyone descrive how the
statistical info below are calculated?
In literature I see for instance electrostatics is reported as: XXX + / -
Y. Where Y is deviation or something like that. Which of the RMSD or
Tot-Drift is giving Y ?
Dear experts,
I have successfully installed a normal gromacs 4.5.4 installation on one of
my machines.
I have read the Installation Instructions that As of GROMACS 4.5, threading
is supported, so for e.g multi-core workstations, MPI is no longer
required.
Does this mean that there is no longer
Hello,
I have a quick enquiry whether temperature affects pontetial energy terms.
Does T is accounted for to parametrize OPLS FF? Do bonded and nonboded
energies vary with T?
Thanks,
Jennifer N.
--
gmx-users mailing listgmx-users@gromacs.org
I have a quick enquiry whether temperature affects pontetial energy
terms. Does T is accounted for to parametrize OPLS FF? Do bonded and
nonboded energies vary with T?
Have you tried?
Try to read up on heat capacity.
Hi David,
Yes it affects potential. My question is whether this
Hello,
I am trying to obtain the density for my system that is exactly identical to
experimental value but whatever pressure I apply density is still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.
--
gmx-users mailing listgmx-users@gromacs.org
Hi David,
I used to apply NPT to fix the density, how can I get the denisty using NVT?
On 20 April 2011 13:46, David van der Spoel sp...@xray.bmc.uu.se wrote:
On 2011-04-20 19.40, Juliette N. wrote:
Hello,
I am trying to obtain the density for my system that is exactly
identical
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