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 listgmx-users@gromacs
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 co
H-C=)
* opls_143 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 wrote:
>
>
> On 4/4/13 6:17 PM, Juliette N. wrote:
>
>> Hi Justin,
>>
>> Thanks a lot for
. I would really appreciate 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 wrote:
>
>
> On 4/4/13 11:38 AM, Juliette N. wrote:
&
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 ETY
-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 wrote:
>
>
> On 4/1/13 7:22 PM, Juliette N. wrote:
&g
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
0.00
s share directory.
;
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
---
On 31 March 2013 12:24, Justin Lemkul wrote:
>
>
> On 3/31/13 12:23 PM, Juliette N. wrote:
>
>> Dear gmx users,
>>
>> Does a
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.
--
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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
for naive questions!
On 21 February 2013 19:23, Justin Lemkul wrote:
>
>
> On 2/21/13 6:58 PM, Juliette N. wrote:
>
>> Hi Matthew,
>>
>> Thanks for your reply. I tried g_analyze as you suggested:
>>
>> 1) I am wondering why the average given by g_en
ties are not small
> or are very asymmetric about 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, 20
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 comments,
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 rea
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 pot
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 pot
t 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
wrote:
>> On Wed, Oct 10, 2012 at 10:24 PM, Juliette N.
wrote:
>>> Hi again,
>>>
>>&g
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 box
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
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 1.3 Gb of memory, which by i
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 wrote:
>
>
> On 8/13/12 4:54 PM, Juliette N. wrote:
>>
>> Hi all,
>>
>> My cpt file doesnt conta
Velocities 1
Forces 0
Box 1
Is this a valid cpt file?
Thank you,
On 13 August 2012 16:36, Justin Lemkul 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
Thanks, maybe I should re start ... :(
On 13 August 2012 16:36, Justin Lemkul 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 ~ 4
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...
I am using 4.5.4. I tried both with and without -append.
On 13 August 2012 16:19, Justin Lemkul wrote:
>
>
> On 8/13/12 4:16 PM, J
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 wrote:
>
>
> On 8/13/12 4:08 PM, Juliette N. wrote:
>
...
Any ideas..
Thanks
On 13 August 2012 15:51, Matthias Ernst 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"
ergy, trajectory, log, etc).")
>
> 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 w
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 Last frame -1 time 7468.965
Also on the gmx site it is sta
On 17 May 2012 05:10, Erik Marklund 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
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. Sin
April 2012 20:58, Mark Abraham 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
>
/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 wrote:
>
>
> Juliette N. wrote:
>>
On 1 April 2012 20:17, Mark Abraham 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
>>
Hi all,
Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt?
Best,
-- Forwarded message --
From: Juliette N.
Date: 1 April 2012 22:10
Subject: Re: [gmx-users] mdrun -rerun
To: Discussion list for GROMACS users
On 1 April 2012 22:07, Mark Abraham wrote
On 1 April 2012 22:07, Mark Abraham 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 -
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 Abraham wrote:
>>>
>>> On 2/04/2012 10:10 AM, Juliette N. wrote:
>&
On 1 April 2012 20:17, Mark Abraham 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
>>
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
appropria
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 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
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 24 February 2012 16:52, Justin A. Lemkul wrote:
>
>
> Juliette N. wrote:
>
>>
>>
>> On 23 February 2012 21:18, Mark Abraham > mark.abra...@anu.edu.**au >> wrote:
>>
>>On 24/02/12, *"Juliette N." *><mailto:joojoojo.
On 23 February 2012 21:18, Mark Abraham wrote:
> On 24/02/12, *"Juliette N." * wrote:
>
>
>
> On 23 February 2012 20:07, Mark Abraham wrote:
>
>> On 24/02/2012 10:55 AM, Juliette N. wrote:
>>
>> Hi all,
>>
>> My average size is 2.9 nm
On 23 February 2012 20:07, Mark Abraham 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
> vi
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
Sorry I meant he default rcoulomb-switch is 0. I am using OPLSAA. Just
confused 0.1 nm switch distance to rc=1.1 doesnt give artifact. I think i
am confusing this with the buffer zone needed between rc and rlist!
On 18 February 2012 10:21, Mark Abraham wrote:
> On 19/02/2012 2:01 AM, Julie
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
Thanks. That was a new thing for me to learn.
On 15 February 2012 23:19, Mark Abraham wrote:
> On 16/02/2012 3:14 PM, Juliette N. wrote:
>
>
>
> On 15 February 2012 23:05, Mark Abraham wrote:
>
>> On 16/02/2012 2:08 PM, Juliette N. wrote:
>>
>>
>>
On 15 February 2012 23:05, Mark Abraham wrote:
> On 16/02/2012 2:08 PM, Juliette N. wrote:
>
>
>
> On 15 February 2012 21:00, Mark Abraham wrote:
>
>> On 16/02/2012 12:22 PM, Justin A. Lemkul wrote:
>>
>>>
>>>
>>> Juliette N. wrote:
&g
On 15 February 2012 21:00, Mark Abraham 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
&g
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 = 0
On 13 February 2012 20:20, Mark Abraham 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 bee
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 cuto
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 be
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.
--
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Please search the archive
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 re
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.
--
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Please search the
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
On 10 September 2011 18:03, Justin A. Lemkul 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
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 6 September 2011 15:42, Dr. Vitaly V. Chaban 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
> minimum (bon
On 6 September 2011 15:03, Justin A. Lemkul 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
>> e
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 bonded
On 26 August 2011 15:17, Justin A. Lemkul wrote:
>
>
> Juliette N. wrote:
>
>
>>
>> On 26 August 2011 13:25, Dr. Vitaly V. Chaban > vvcha...@gmail.com>> wrote:
>>
>> >>. Now it is clear that
>> >> the sum of [ LJ
On 26 August 2011 13:25, Dr. Vitaly V. Chaban 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 interact
On 26 August 2011 12:06, Justin A. Lemkul 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
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 *inter*mo
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 I
. Lemkul 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
>&
July 2011 14:53, Justin A. Lemkul 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
>> (
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 the
:
>
>
> Juliette N. wrote:
>
>> 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
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 ste
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 if
Hello all,
I have a quick question about extracting energy values from g_energy. I used
an old trajectory to extend my simulation from 1 ns to 5 ns. Energy values
from extended run do not take into account values of the first 1 ns. Is
there any way to combine energies of these two runs? or I shoul
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 ?
g_energy
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps
I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560, max 72.359520 (between atoms 314 and 315)
bo
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
>
>> 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 whethe
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.
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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 wrote:
> On 2011-04-20 19.40, Juliette N. wrote:
>
>> Hello,
>>
>> I am trying to obtain the density for my system that is exactly
>
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.
--
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Hi everyone,
I have a question about -nmol option of g_gyrate -h :
With the -nmol option the radius of gyration will be calculated for multiple
molecules by splitting the analysis group in equally sized parts.
If there are 4 chains ABCD in the solvent, and each chain has n atoms of
different typ
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