You can refer to following papers:
HALVOR S. HANSEN, PHILIPPE H. HÜNENBERGER , JComput Chem 32: 998?1032, 2011
and
?
ROBERTO D. LINS, PHILIPPE H. HUNENBERGER. J Comput Chem 26: 1400 ?1412, 2005
Nisha
Quoting ABEL Stephane 175950 :
Dear All,
I am looking
Here are few papers you can refer to:
Gromos forcefield for hexopyronase-based carbohydrates - Roberto
D.Lins and Philippe H. Hunenberger 2005
(In gromos forcefield there are parameters for galactose)
An improved OPLS?AA force field for carbohydrates- D Kony 2002
Hope it helps!
N
Thanks Tsjerk! Looks like it is working!
Quoting Tsjerk Wassenaar :
Hi Nisha,
For building you can also use pymol if you have it installed. On the
command line you can issue:
pymol -qcd
'editor.build_peptide("GGG");cmd.save("triglycine.pdb","not hydro")'
Hope it helps,
Tsjerk
On Mon,
Thanks Justin!
Nisha P
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hello,
I want to simulate n-glycines (diglycine, triglycine..etc) I
tried to get the structure from PRODRG, but the program adds H's on
the N-terminal instead of on C- terminal. Is there another pr
Hello,
I want to simulate n-glycines (diglycine, triglycine..etc) I tried
to get the structure from PRODRG, but the program adds H's on the
N-terminal instead of on C- terminal. Is there another program I could
use, or a site where I could get the structure of oligoglycines? For
exampl
I am not sure if you have looked through this paper, but it gives the
parameters for sugars.
A new GROMOS force field for hexopyranose-based carbohydrates by RD Lins, 2005
A biomolecular force field based on the free enthalpy of hydration and
solvation: The GROMOS force?field parameter sets
I know and I apologize, I mistyped. It is an isolated molecule. I did
try to combine the parameters of OPLSAA of carbohydrates(Jorgensen,
1997) with the nucleotide base paper (Jorgensen, 1991). However, I am
not sure the partial charge that I should use on the Carbon (C) atom
of the sugar
I apologize, but I am trying to simulate Cytidine (not cytosine). The
parameters are given for cytosine.
Nisha
Quoting David van der Spoel :
On 2011-03-18 20.14, nishap.pa...@utoronto.ca wrote:
Hello,
I am trying to use OPLS-AA force field for simulating nucleosides eg.
cytosine, adenosi
Hello,
I am trying to use OPLS-AA force field for simulating nucleosides
eg. cytosine, adenosine etc. I found parameters for nucleotide bases
(eg. 1-methylcytosine) but I haven't been able to find parameters for
nucleosides. Does anyone know where I can find parameters for
nucleotides
Hi,
I am trying to simulate hexopyronase using OPLS-AA forcefield
using parameters from the paper:
An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.
The set of torsional angle parameters in the paper are given in
Kcal/mol, but because I am using OPLS-AA I would need to
Thanks Justin!
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hello,
I am trying to simulate hexopyronase using OPLS-AA forcefield
using parameters from the paper:
An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.
I was looking through the ffoplsa
Hello,
I am trying to simulate hexopyronase using OPLS-AA forcefield
using parameters from the paper:
An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.
I was looking through the ffoplsaabon.itp file and there are some
dihedral parameters for hexopyronase. I am not s
Thanks Justin!
I am using constraints, but like you said it could be just
PBC. I did compare some of my calculations to experimental values and
they are fairly similar.
Nisha P
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hello,
I ran a simulation of one mo
Hello,
I ran a simulation of one molecule of galactose (cyclic) in water.
After the simulation run, when I checked the trajectory file in VMD,
the bonds in the galactose molecule stretched and during the run
changed back to its original starting form. I am using GROMOS force
field ffG5
Thanks. I am going to look over it. But I was wondering is it possible
to just simulate one molecule of sucrose (glucose+fructose) in water
using any of the force fields by Gromacs? I realize I would have to
add the parameters to the .rtp files, but as you mentioned that the
force fields re
Hello,
I am trying to simulate galactose in water using Gromos FFG53A6
force field. The molecular formula for galactose is C6H12O6, however
in the FFG53A6.rtp file, the molecular formula is C6H10O5 for
galactose-A and B. Why is it different? I would really appreciate some
help!
Thank
Hello,
I am trying to simulate galactose in water using Gromos FFG53A6
force field. The molecular formula for galactose is C6H12O6, however
in the FFG53A6.rtp file, the molecular formula is C6H10O5 for
galactose-A and B. Why is it different? I would really appreciate some
help!
Thank
Quoting ms :
I did two different simulation. One with van der Waals attractive term
and one without van der Waals attractive term. And so to see the
difference between the LJ potential between the two simulation I
wanted to plot the LJ potential for both the simulations and
superimpose th
Quoting "Justin A. Lemkul" :
I actually want to plot my simulation with ad without the attractive
term C6 of van der Waals and superimpose them to see the difference.
nishap.pa...@utoronto.ca wrote:
Quoting "Justin A. Lemkul" :
How does sigeps read the input file? I tried using sigeps to
Quoting "Justin A. Lemkul" :
How does sigeps read the input file? I tried using sigeps to plot
LJ for different solutes in solvent and it gives me the same C6 and
C12 value, when it runs, which seems a weird.
c6= 1.0e-03, c12= 1.0e-06
sigma = 0.0, epsilon =
Hello,
Is there an option to plot Lennard Jones potential? I tried
looking through the list and manual but I did not find any suggestions
on how I could plot a LJ 6-12 potential plot.
Nisha
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I see. It did work . Thanks a lot Justin!
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Quoting "Justin A. Lemkul" :
Thanks Justin! I do want the non-bonded potential between my solute
and solvent. So in my .mdp file I put my solute and solvent as
energygrps and ran mdr
Quoting "Justin A. Lemkul" :
Thanks Justin! I do want the non-bonded potential between my solute
and solvent. So in my .mdp file I put my solute and solvent as
energygrps and ran mdrun using this command:
mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)
Is that correct
Hello,
I want to plot the interaction potential energy between my solute
and solvent. In my .mdp file I did not mention anything under
energygrps,so I am thinking it calculates the energies for the whole
system. But is there a way I can extract say for example LJ-14 term
between my sol
Would I change the sigma to negative in my nb.itp file the way it is
set or do I need to include a [nonbond_params] section and make sigma
negative in that specific section? because I realize from the manual
OPLS-AA uses combination rule 3 but in the manual it shows to combine
sigma for i a
I am going to give that a try. Thanks.
Quoting Berk Hess :
Hi,
Maybe it is not so clear from the topology table in the manual, but
when you supply
sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params
section also expects sigma and epsilon.
So it seems you could not
I see. I actually want to compare my RDFs with C6 term off. Earlier I
tried using force.c code file and turned C6 = 0, but when i compared
my RDFs, it didn't look any different so I am not sure if it even
worked at all or made any difference to the simulation, but again I
was using OPLS-AA
I ran the simulation using a different force field ffG53a6. I modified
the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded
parameters, but this time for urea in water. The simulation ran fine
without any warning or exploding. I don't understand why it would work
with one fo
I tried using the nonbonded parameters as defined below in my
ffoplsaanb.itp file for methanol in water and this is the syntax I used:
[nonbond_params ]
;i j funcc6 c12
opls_154opls_111 1 0.00E+000 2.43E-006
opls_154opls_112 1 0.00E+000
Okay I am going to give it a try. I just wanted to make sure I was
calculating C6 and C12 correctly as well using sigma and epsilon
according to rule 3
C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon
Thanks
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hello,
I have a co
Hello,
I have a concern regarding C6 attractive term in LJ potential. I
am using OPLS-AA force field, and I wish to turn off attractive term
C6 by setting the parameters to zero. One of the suggestion was to add
a [nonbond_params] in my ffoplsaanb.itp file and set the C6 to zero
betwee
Hello,
It doesn't contribute as such. I was using a different force
field before OPLSAA and it was all atom so I could make the charges
zero in the topology file, I wanted to do the same.
Quoting "Justin A. Lemkul" :
Mark Abraham wrote:
On 16/11/2010 7:14 AM, nishap.pa...@utoronto.
Hello,
I want to turn off electrostatic interactions between CH4 and SOL
in my system. I am using ffG53a6 forcefield for CH4 and spc for my
water model. CH4 is an united atom and so I can't make the charges
zero in the topology. Is there any other way I can turn off
electrostatic inter
How can I do that using OPLSAA, because in the nb.itp file the values
are for sigma/epsilon? Can I change C6=0 in the code file?
Quoting David van der Spoel :
On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote:
Hello,
Is there a way to turn off the 6-term in LJ 6-12 potential?
-Nisha P.
Hello,
Is there a way to turn off the 6-term in LJ 6-12 potential?
-Nisha P.
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Please don't po
I did look at the plot, and it shows that the curve is smoothing right
under zero at -1.00e+05 but then why does the average potential show a
positive number? Shouldn't that number be negative as well?
Quoting David van der Spoel :
On 2010-09-20 19.58, nishap.pa...@utoronto.ca wrote:
Hello
Hello,
I am simulating 2M urea in water with single methane (77 urea +
1926 water). I used genbox -ci -nmol to add the number of urea
molecules and then used genbox to add water molecules (as suggested in
the manual). When I tried to do energy minimization this is what I got :
Steepest
Hello,
I am trying to simulate N-methylglycine amide. I selected 'none'
for the termini using oplsaa forcefield. I got the topology but I got
the error saying:
ERROR 1 [file topol.top, line 126]:
No default Ryckaert-Bell. types
I checked the line 126 in my topol file and it is the di
Okay I see what you mean. Thanks alot!
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
I did use this command:
editconf -f md.tpr -mead na.pqr. If I understand it correctly for
-sig56 option, I would use the min rvdw from my mdp and divide it
by 2 and use that value in th
Also, I am using OPLS-AA force field with TIP3P water
Quoting David van der Spoel :
On 2010-08-30 20.32, nishap.pa...@utoronto.ca wrote:
Hello,
I have a question about how gromacs assigns VDW radii for ions. I
checked the vdwradii.dat file but it does not mention any ions, so where
do the par
I did use this command:
editconf -f md.tpr -mead na.pqr. If I understand it correctly for
-sig56 option, I would use the min rvdw from my mdp and divide it by 2
and use that value in the command line?
Quoting David van der Spoel :
On 2010-08-30 20.32, nishap.pa...@utoronto.ca wrote:
Hell
Hello,
I have a question about how gromacs assigns VDW radii for ions. I
checked the vdwradii.dat file but it does not mention any ions, so
where do the parameters for ions come from? I got the .pqr file for
sodium and I got the atomic radii of 1.6652A, I am not sure where that
value c
Thanks! I did overlook that.
Quoting David van der Spoel :
On 2010-08-24 22.53, nishap.pa...@utoronto.ca wrote:
Hello,
I converted a .tpr file for Bromine ion and Potassium ion using -mead
option and editconf. It gives out the Van der Waals radius of the atom,
but I don't understand why i go
Hello,
I converted a .tpr file for Bromine ion and Potassium ion using
-mead option and editconf. It gives out the Van der Waals radius of
the atom, but I don't understand why i got ~2.46A for Potassium and
~2.31A for Bromide. Isn't the bromide ion bigger than Potassium? And I
used ge
I believe the bonds are not defined in the OPLS-AA force field for
NaCl. I know this might sound like a stupid question, but is there a
way to determine the bond force constant (kb), I tried to look it up,
but I couldn't find anything.
Quoting "Justin A. Lemkul" :
nishap.pa...@utoront
Hello,
I want to simulate a simple NaCl ion in water. I know the method
using genion which adds individual Na+ and Cl- ion, but I wish to
simulate Na-Cl connected rather than free ions floating in water. When
I ran the grompp command I got the error:
No default Bond types
So I am think
Thanks. I am definitely going to look into that.
Quoting chris.ne...@utoronto.ca:
Nisha:
Simply applying available tools and seeing if the distribution looks
okay is not a good plan. You should have a very well-defined idea of
what you are trying to test and then pick a tool to get that done.
Well I guess, what I am trying to get at is, for my system I want to
make sure that 100ns has covered all the conformational changes within
the molecule, although I know there is not that much conformational
changes for glycine molecule, but I just wanted to confirm. I did run
g_angle comma
So is there a way I can test for convergence for my zwitterion for 100ns run?
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for
one glycine zwitterion in water. for g_rama I didn't see anything
in xmgrace, and
Okay so I tried to analyze the torsion using g_chi and g_rama for one
glycine zwitterion in water. for g_rama I didn't see anything in
xmgrace, and same for g_chi. I used this command for g_chi
g_chi -f traj.xtc -s gly.gro -phi -psi
When I run the command it says 1 residue with dihedrals fou
Hello,
I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is th
Hello,
I ran a simulation for 100ns on 2 nodes (16 cores). I tried to
generate replicates with different starting trajectories and ran it on
one core, so basically I have 64 replicates with different starting
trajectories and I am using 8 nodes. I wish to combine all the .xtc
files fro
Thanks Mark, I did play around with the -npme option a little and
turns out using -npme 1 works for the system this is mdrun command I
have in the script file
mdrun_openmpi -nosum -dlb yes -npme 1 -cpt 40 -maxh 48 -deffnm md
Thanks.
Quoting Mark Abraham :
- Original Message -
From:
Thanks Justin. But how come it worked for methanol. The system is of
the same size , and all the parameters are same, so I don't understand
why it won't work for ethanol.
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hello,
I got this following error when I was trying t
Hello,
I got this following error when I was trying to run a simulation
of ethanol-water box size 4*4*4 nm (~6530 atoms).
Fatal error:
There is no domain decomposition for 14 nodes that is compatible with
the given box and a minimum cell size of 0.62175 nm
Change the number of nodes or m
Hello,
I have a concern regarding what -settime actually does. I ran
replicates of same simulation with different starting trajectories,
basically to get more sampling. Now I wish to combine all the .xtc
files from each replicates so I can analyze it as a whole. Now what's
the differen
Hello,
I am not sure if anyone else has some experience with this, but I
want to simulate a hard sphere in a solvent (water and heptane). I
believe for the hard spheres, the attractive terms for LJ potential is
very negligible so the only term to take into account is repulsion,
from wh
I am trying using prev_md.cpt file. I checked and it looks okay, so
hopefully it will work. If not I will try using .trr files.
Thanks
Quoting Tsjerk Wassenaar :
Hey,
Otherwise it's also still possible to do old style continuation with a
frame from the .trr/.edr file, provided you have tho
Hi Justin,
Well the way I continued my second part of the simulation was
using my md.cpt file. I checked my .cpt file and this is what I got:
Last frame -1 time 83786.961 , so I guess my second run
updated the file, so does this mean I have to do the whole simulation
again? or c
Hello,
I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)
Checking file md.part0002.xtc
Reading frame 0 time 48190.004
# Atoms 6533
Precision 0.001 (nm)
Reading frame 178000 time 83790.008
Part one of the simu
I am using gromacs-4.0.5.
Thanks.
Quoting XAvier Periole :
That looks like a nice bug!
You should specify which gmx version you are using. That would help
getting it fixed.
On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote:
Hello,
I am a running a simulation of 100ns, so I have
Hello,
I am a running a simulation of 100ns, so I have two edr files
md.edr and md.part0002.edr. When I calculate some of the energy values
using g_energy for each of the .edr files individually I get the
following result:
For md.edr:
Statistics over 27120401 steps [ 0. thru 54240.8
Hi Zuzana,
You are right. I did get my density to ~0.986g/cm3, and I
actually came across this other paper by Price and Brooks, and
initially they get a density of Tip3p using pme at around 0.979g/cm3,
but they tweak some of the parameters in oplsaa to get the correct
density. I am n
Hello,
So I looked at the manual and I changed my mdp parameters as
follows to equilibrate at a constant pressure.
RUN CONTROL PARAMETERS =
integrator = sd
tinit= 0
dt = 0.002
nsteps = 50
nstcomm
Thanks. I will look up the manual again.
Quoting Sander Pronk :
Hi Nisha,
Looking at your .mdp, there are some issues that might lead to the
behavior that you describe:
First: you should try to look up the published densities for tip3p
water at 300K - they might actually be close to what
I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density
when I create the box using genbox is 997.177g/l. I did energy
minimization run and the potential energy did converge smoothly, so I
did NPT equilibration run of 100ps and I got the density value of
975g/l. Why does the de
Quoting Mark Abraham :
On 31/03/2010 5:19 AM, nishap.pa...@utoronto.ca wrote:
Hello,
I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My
simulations are 100ns each. I am using different cut-off. i.e
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0, 1.2 and 1.3
and these are my para
Hello,
I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My
simulations are 100ns each. I am using different cut-off. i.e
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0, 1.2 and 1.3
and these are my parameters for Pressure coupl
What do you mean the value for methane? As in the charges? This is my
topology file and I am using OPLS-AA for methane.
Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Namenrexcl
Methane3
[ atoms ]
; nr type resnr residue atom cgnr
I am trying to get an rdf graph actually, and my values are very close
to one, but not exactly one, and I was wondering if there is some
normalization issue with g_rdf? These are my values for rdf:
0 0
0.002 0
0.004 0
0.006 0
0.008
Hello,
I am simulating one methane molecule in 899 water molecues in the
box size of 3 3 3 nm (27nm^3). I would like to determine density vs
time. Is there a way I can do that? I am running my simulation at
constant Volume i.e. no pressure coupling. I tried using g_density but
it give
Hi Justin,
Well from the previous post:
The number density for water should be about 32.5 waters per cubic
nanometer. So if my box size is 4 4 4 =64nm^3, then shouldn't number
of water molecules be 64*32.5 = 2080? May be I am not understanding it
correctly. I am using Tip3p water
Hello,
I am trying to use genbox to add water molecules to my system
consisting of one molecule of ethane in the box size of 4 4 4nm(
64nm^3). If I understand it correctly, with the system of that size, I
should have ~2080 water molecules in my system, but instead genbox
adds ~2177 mo
Quoting David van der Spoel :
On 3/3/10 8:14 PM, nishap.pa...@utoronto.ca wrote:
Hello,
I am trying to simulate Ethanol in water using OPLSAA. I already
tried it with all atoms, but now I want to try it with United
atoms for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I
cr
Hello,
I am trying to simulate Ethanol in water using OPLSAA. I already
tried it with all atoms, but now I want to try it with United atoms
for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I created
the topology but I got an error saying 'No bond types', so I checked
ffoplsaa
Hi,
I am trying to extend my simulation time from 100ns -> 300ns. So I
used the command :
tpbconv -s old.tpr -extend 10 -o new.tpr
but I got this:
Extending remaining runtime of by 20 ps (now 14992 steps)
Writing statusfile with starting step 0 and length 14992
okay this should work
http://docs.google.com/fileview?id=0B_QNmYARywUiNzE0MDA0NWMtYjFiMy00MTRjLThkNDMtNTk3NDgyNjcxZTgx&hl=en
-Nisha
Quoting chris.ne...@utoronto.ca:
I didn't get the attachment. Please upload the image to some website
and post the link.
--original message --
I saved my r
Hi,
I saved my rdf plot as a pdf file and I have attached it to this
email. Hopefully it will work. My system is one methane with 893
molecules of tip3p water in a cubic box of size 3 3 3 (nm). My
topology file is :
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetyp
Hi Will,
I have been using pme from the very start and it didn't help with
the volume. Could you please elaborate on what you mean by average
g(r) over every molecule?
And because my rdf-s are not smooth enough even with 100ns, I get
fluctuating data using rdf-s.
-Nisha
Quoti
Hi,
I am doing rdf's of simple molecules. I ran my simulation of water
and methane for 100ns to get a smoother curve for the rdf. I am trying
to determine the volume, and after a certain cut-off I would assume my
values to be constant (i.e. volume), but the values fluctuate alot
(i.e. d
Hello,
I am running rdf simulations, and I tried running simple methane
using OPLS-AA force-field for 100ns. I was hoping to get a smoother
curve for such a small molecule in 100ns. Could someone please look
over my mdp parameters and suggest if I am missing something.
Thanks.
Nisha
I see what you mean, so say if I am doing RDF, the values beyond 9A
would be bogus?
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hello,
I wanted to know, if say my box is 30A (cubic) and if I set my
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that
Hello,
I wanted to know, if say my box is 30A (cubic) and if I set my
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean,
the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm
(to get half the box cut-off)? I am a little confused about that.
Thanks.
Hello,
I created a topology file for 1 ammonia in water. Could someone
please have a look at the file and let me know if it looks okay.
Thanks
Nisha Patel
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Namenrexcl
Ammonia 3
[ atoms ]
;
Hello gmx users,
After running energy minimization steps, I got the following error:
teepest Descents:
Tolerance (Fmax) = 1.0e+00
Number of steps= 100
Step=0, Dmax= 1.0e-02 nm, Epot= -2.84750e+04 Fmax= 1.53401e+04,
atom= 2501
Step=1, Dmax= 1.0e-02 nm, E
I have a question regarding the simulations that I am running. I tried
creating a pdb file with one methane and water molecules, but the
system keeps showing 'bad contact' error when I run the minimization
step and I don't understand what I am doing wrong.
This is my methane file :
TITLE
Does anyone know where I can get a pdb file for ammonia? I tried
searching but I am not sure if there is a website for the pdb files I
can use in gromac. Any suggestions would be helpful.
Thanks.
Nisha
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HI,
Okay, so I am trying to plot rdf of one methanol this time in water.
Is there a way to select methanol molecule as a whole (i.e. get rdf
from the center of the molecule), instead of Me, O and H. Even though
I put Me, O and H in same group, I am getting a weird rdf plot
(Attached to t
Hi,
You are right, I had to delete some water molecules, it is working fine now.
Thanks.
-Nisha P
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Hi Justin,
I am trying to plot rdf of one methane molecule in water (spc
water, 1095(water molecule in my file). I did cre
Hi Justin,
I am trying to plot rdf of one methane molecule in water (spc
water, 1095(water molecule in my file). I did create the file using
genbox (31.010 31.010 31.010). This is the energy minimization file I
am using:
title = Methane in water
cpp = /lib/cpp
in
Hi, I tried energy minimization and I am getting the error while I am
running the minimization step. But then I still tried to carry on with
normal md-simulation, and it was fine, but I am sure it won't give me
the result that it should. Is there a reason for that? I have tried
very low ene
- Forwarded message from nishap.pa...@utoronto.ca -
Date: Mon, 14 Dec 2009 14:06:30 -0500
From: nishap.pa...@utoronto.ca
Reply-To: nishap.pa...@utoronto.ca
Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep
To: "Justin A. Lemkul"
I tried to run mi
Hi,
I am trying to run a simulation with 1360 Tip4p water molecules and
one methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541
atoms) but I am getting the error:
t = 0.000 ps: Water molecule starting at atom 5433 can not be settled.
Check for bad contacts and/or reduce the ti
Hi!
Does anyone know how I can turn off the coulomb interactions in the
.mdp file? I tried to change the values of rcoulomb to 0, but it
doesn't work.
Thanks
NP
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