Hi all,
Does anyone know of way I can use Gromacs to calculate the disasociation
constant of a calcium ion held by two loops in a protein in water
simulation? my starting point was a pdb file of the protein with the bound
ions in place. Eventually I would like to evaluate the time constant
(meaning
Dear gromacs users
I did simulation of protein-dna by gromacs and amber03 force field. I want
to do some analysis by amber. what is the best way for conversion of gromacs
trajectory and topology files to amber files?
any help will highly appreciated.
--
Leila Karami
Ph.D. student of Physical C
Ah, sorry, I didn't read you well enough.
I've just seen that GROMACS 4.5 introduced trjconv -round to address this kind
of issue. I suppose you will find trjconv -round -split works for you.
Mark
Hi, Mark
Thank you for your suggestion.
I'm sorry that my version is 4.0.5
I think I can use -
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On 12/07/10, Hsin-Lin Chiang wrote:
>
>
>
>
>
>
>
>
>
>
> Hi, Mark
>
>
>
> Thank you for your reply.
>
> I know -skip -sep is more robust.
>
> Since the definition talked about nr-th frame but not nr-th ps.
>
>
>
> -skip int 1 On
Hi, Mark
Thank you for your reply.
I know -skip -sep is more robust.
Since the definition talked about nr-th frame but not nr-th ps.
-skip int 1 Only write every nr-th frame
-[no]sep bool no Write each frame to a separate .gro, .g96
or .pdb file
The problem is that -s
Dear users,
While installing gromacs-4.5.3 I got an error on executing make command. I
am installing this gromacs version on cygwin. The error written below,
please tell me about the error where I was wrong
Creating library file: .libs/libgmx.dll.a
.libs/checkpoint.o:checkpoint.c:(.text+0xcd):
On 12/07/10, Hsin-Lin Chiang wrote:
> Hi,
>
> My time unit is 1ps and today I have 300ns data generated by parallel
> simulation.
> I use trjconv -split 1000 on my trajectory but get the truncated end at t=
> 5000.0
> Theoretically it should stop at t= 1000.000
> I found that I don't ha
Hi,
My time unit is 1ps and today I have 300ns data generated by parallel
simulation.
I use trjconv -split 1000 on my trajectory but get the truncated end at
t= 5000.0
Theoretically it should stop at t= 1000.000
I found that I don't have t= 1000.0 frame but have t= 1000.6,
2000.0
nishap.pa...@utoronto.ca wrote:
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
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
On 06/12/10 23:26, nishap.pa...@utoronto.ca wrote:
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.
The expression "plot my simulation" makes no sense. You don't plot a
simula
Hassan Shallal wrote:
Dear Gromacs users,
I have some concerns about the both the pressure fluctuations and
averages I obtained during the equilibration phase. I have already read
through several similar posts as well as the following link
http://www.gromacs.org/Documentation/Terminology/P
Dear Gromacs users,
I have some concerns about the both the pressure fluctuations and averages I
obtained during the equilibration phase. I have already read through several
similar posts as well as the following link
http://www.gromacs.org/Documentation/Terminology/Pressure. I understand the
> Subject: [gmx-users] MOPAC gromacs mdreun error (vidhya sankar)
> To: gmx-users@gromacs.org
> Message-ID: <665887.73042...@web95501.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gerrit sir,
> Thank you for your atonce reply
> my mopac stand alone binar
On 12/07/10, nishap.pa...@utoronto.ca wrote:
> 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.
>
g_sigeps -c6 0 probably does that. See g_sigeps -h
Mark
>
> >
> >
>
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
nishap.pa...@utoronto.ca wrote:
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
sig
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 =
swagata chakraborty wrote:
Hi,
Thanks a lot for the reply and the suggestion.
I am carrying the simulation in 100% DMSO( no water) at 318 K.the em.mdp
file is as follows:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002
nishap.pa...@utoronto.ca wrote:
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.
g_sigeps
-Justin
Nisha
--
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
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx
Hi,
Thanks a lot for the reply and the suggestion.
I am carrying the simulation in 100% DMSO( no water) at 318 K.the em.mdp
file is as follows:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002; time step
nsteps
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
re posting!
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>
> -- next part --
> An HTML att
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 mdrun using this command:
mdrun -s md1.tpr(including energygrps) -rerun md.xtc
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
nishap.pa...@utoronto.ca wrote:
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 exa
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
Hi again,
unfortunately I would need the constraint for a large number of molecules, say
~1000 i.e. 2000 vsites representing a few atoms each.
The constraint length should however be the same for each molecule.
Assigning groups for each constraint group would not be possible due to the
grou
Dear Gerrit sir,
Thank you for your atonce reply
my mopac stand alone binary works well i have tested using ./run_mopac7
tests/force
but mdrun is not properly linked aganist libmopac.a
i am using the following command to configure
./configure --disable-float --without-qmmm-mopa
Hi,
Unfortunately constraints can not be applied to virtual sites and grompp
apparently
does not not check for this. I will add a check.
Constraints between virtual sites can lead to very complex constraint equations
between the masses involved. Thus the general case if difficult to implement.
Y
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service. I am CC'ing the list and would ask that anything
further be posted there.
Before posting anything to the list, check the list archive. Your problem has
been posted and answered literally
On 6/12/2010 9:43 PM, Sebastian Fritsch wrote:
Hi everybody,
I have some trouble setting up topology for my, I admit, quite unusual
system. I need to constrain the center of masses of two groups of
atoms to a fixed 'bond' length. Since I have to do this for every
molecule I cannot use the 'p
Hi everybody,
I have some trouble setting up topology for my, I admit, quite unusual
system. I need to constrain the center of masses of two groups of atoms
to a fixed 'bond' length. Since I have to do this for every molecule I
cannot use the 'pull constraint' of the free energy code.
Thus
Dear All,
I am working on the interaction of a positively charged peptide (18AA) and the
bacterial membrane consisting of a mixture of zitterionic and negatively
charged lipids. Our experiments show that the peptide can disrutp the membrane.
One problem puzzed me is that which method to use i
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