Hello,
I have done COM pulling simulation to pull a small molecule
(5-Fluorouracil) through a path. I want to see the rotational freedom for
the pulled over molecule during the SMD simulation. Is it meaningful to
calculate the rotational autocorrelation for a molecule which observes
external force
Hello,
I got a PMF curve like 0...-2...022. its converged at 22. I have a
doubt in the final deltaG value, for this curve the deltaG is 22-2 or 22-0.
Regards,
Vijay.
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Hello,
I have done umbrella sampling for 10ns on 23 windows and g_wham program
shows converged histograms and PMF curve. I used the following g_wham
command,
g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -o profile.xvg
-hist histo.xvg -b 1000 -e 1
I considered first 1ns simulation
Hello,
I am trying to find the PMF for the diffusion of small molecule through a
nanotube. I have generated the umbrella sampling windows from
pull_geometry=direction simulation and umbrella sampling with
pull_geometry=position. I guess the PMF for this system can be obtained by
combining the g_wh
plain; charset=ISO-8859-1; format=flowed
>
>
>
> Vijayaraj wrote:
> > Hi,
> >
> > What is the relation between pulling force and free energy of binding.
> > can we relate the maximum pulling force with the free energy. for
> > example, 2 systems has the maximum pul
Hi,
What is the relation between pulling force and free energy of binding. can
we relate the maximum pulling force with the free energy. for example, 2
systems has the maximum pulling force and free energy as below from
umbrella sampling and g_wham analysis,
max. force
Hello,
I am studying the diffusion of a small molecule through a cyclic peptide
based nanotube using pull code, here is my code for pulling,
pull= umbrella
pull_geometry = position
pull_vec1 = 0 0 1
pull_start = yes
pull_ngroups= 1
pull_group0 = Protein
pull_group
CS users
> Message-ID: <4eb7f727.3000...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Vijayaraj wrote:
> > and also I tried to plot the PMF curve from this data, I got few warning
> > messages like "no data point in bin 20, You may
at
0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm window
to get the restrain distance converged?
On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj wrote:
> Hello,
>
> Thanks for the suggestions. I did umbrella simulation for 20ns and the
> pull force is as below.
>
&
Hello,
Thanks for the suggestions. I did umbrella simulation for 20ns and the pull
force is as below.
19960.-6.78192
19962.33.3579
19964.-3.1808
19966.-15.0304
19968.-55.4436
19970.-38.9422
19972.-9.41927
19974.-5.95981
19976.
Hello,
I have done umbrella sampling with "pull=umbrella" and I found that the
pulling group has high fluctuations and sometimes moving out of the
periodic box. I think that the harmonic potential is not properly applied
and thus the pulling group is not retained with the specified COM distance
be
Hello,
Can we restart the umbrella sampling simulation after some 10 or 15ns
simulation using the cpt and gro files generated from the previous step. I
am not sure whether it will take force generated from the previous step.
Regards,
Vijay.
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Hello,
What is the criteria for umbrella sampling convergence. If I am right, the
pulling force and COM distance should be converged. I do not see force or
COM distance convergence after 10ns of simulation.
Regards,
Vijay
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= 1000
pull_nstxout= 1000
pull_nstfout= 1000
I will do this umbrella sampling for 10ns,
Do you think the COM distance can converge after long simulation time? ie
back to the restraint position.
Regards,
Vijay.
> Vijayaraj wrote:
> > Hello,
> >
> > I am doing
Hello,
I am doing umbrella sampling to calculate PMF curve for the detachment of a
terminal cyclic peptide with 8 aa's (CP) from the self-assembled cyclic
peptide nanotube. I extracted the reaction coordinates staring from 5.5 ang
COM distance between the terminal CP and the 2nd CP to 17.5 ang, I
Hello,
I need to simulate a peptide in nonane solvent environment using ff99SB
force field. As there are different procedures used to create a solvent box,
different from water, specific to several force fields, I would like to make
sure the method which I am going to use will be appropriate for m
Hello Users,
Previous I have done simulation of small protein using Amber10 with ff99sb
force field. I did the same calculation using the gromacs 4.5.1 with amber
ff99sb force field. I found a loop segment takes much more fluctuation with
gromacs simulation and which was not observed with the
Hello,
I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
terminal residues from NALA and CALA to normal ALA (just as middle
residues). As the terminal selection option is not enabled with the amber
ff, I am using the termini modification parameters with aminoacids.c.tdb.
here
want to use the none option for
the terminals (with amber ff). any suggestion?
Regards,
Vijay
Date: Fri, 19 Aug 2011 15:31:04 +0200
> From: Vijayaraj
> Subject: [gmx-users] -ter option with pdb2gmx
> To: gmx-users@gromacs.org
> Message-ID:
> >
> Content-Type: text/pla
Hello,
I am trying to use "-ter" with the pdb2gmx command, seems its not working
fine.
>pdb2gmx -f -o -ter
I also used "-inter" option, its not working.
I am using 4.5.4 version. any help would be greatly appreciated.
Regards,
vijay
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