Dear All,
I am re-posting with some replies to my first message.
> the cell demensions for .gro files are at the bottomn,
you know, you right. There at the top for .pdb file, and it is just a unit
cell, and not very trivial to center graphically.
And when you answere somones question like
There's lots of information in the gromacs manual to show that the
.atp file is not the only file that you must modify. My most important
suggestion to you is that you should read the entire manual, possibly
twice, before attempting to build new molecules.
Gromacs manual, page 96:
5.3.1
Hi,
I am trying to use g_sham to obtain free energy landscape from a simulation.
I can obtain the .xpm files but I want to know if there is any way of
obtaining the actual histogram (in a form of a ASCII matrix vith
numerical values) to use it in some other plotting program to draw
contour lines p
Moeed wrote:
Hello Justin,
I created structure file for a 4-carbon repeating unit as follows:
HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00
20.00 C
HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00
20.00 H
HETATM3 2HAA DRG 1 15.0
Hello Justin,
I created structure file for a 4-carbon repeating unit as follows:
HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00
20.00 C
HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00
20.00 H
HETATM3 2HAA DRG 1 15.050 -4.790 0.326
Hi all,
I am trying to perform umbrella sampling along with the WHAM to get the PMF.
I go over the "umbrella sampling" tutorial prepared by Justin. Everything
seems OK to me except one point. I could not understand the output given by
the hist option of the g_wham command. There, what does "histo
Thanks!
On Tue, Jun 22, 2010 at 2:07 PM, Per Larsson wrote:
> Hi!
>
> You can choose cmap/no cmap when you run pdb2gmx.
>
> /Per
>
> Skickat från min iPhone
>
> 22 jun 2010 kl. 19:24 skrev Sai Pooja :
>
> > Hi,
> >
> > I am using gromacs from the git repository which I downloaded 2 days
> back.
Hi Users,
I am experiencing the following fatal error when I try using the
grompp command.
grompp -f mdout.mdp -r conf.gro -p topol.top
.
.
.
---
Program grompp, VERSION 4.0.99-dev-20100409-004
Source code file: toppush.c, line: 631
Fatal
Hi!
You can choose cmap/no cmap when you run pdb2gmx.
/Per
Skickat från min iPhone
22 jun 2010 kl. 19:24 skrev Sai Pooja :
> Hi,
>
> I am using gromacs from the git repository which I downloaded 2 days back.
> Charmm has been implemented in this version. Is it possible to use the Charmm
>
Dear Elio:
First, you need to convert your PMF to a free energy difference
between states. That means defining a boundary between, for example,
bound and unbound states. The integrate your PMF over the bound and
unbound states to get two dG values, and their difference is your free
energy
Hi,
I am using gromacs from the git repository which I downloaded 2 days back.
Charmm has been implemented in this version. Is it possible to use the
Charmm ff without CMAP with it?
Regards
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
gmx-users mailing listgmx-users@gromac
Moeed wrote:
Dear Justin,
Actually, I used -d option because you said the atoms in the box must be
half a bond length from the edges of box...I thought maybe this can be
done by -d...
My point was that you should not be using a combination of -box, -d, and -angles
simultaneously. Use e
Dear Justin,
Actually, I used -d option because you said the atoms in the box must be
half a bond length from the edges of box...I thought maybe this can be done
by -d...
With PRODRG I am unable to produce coordinate file a chain with less than
three C atoms.
I sketched the molecules:
C-C ethane
Hi,
I recently made up a topology for ADP. You can probably modify it to
ATP easily.
I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm
). The charges are copied from CHARMM27. Also, there is one dihedral
angle missing, again, copied from CHA
Gavin Melaugh wrote:
Hi all
I have a ran a simulation of 64 molecules in a cubic box with side 6 nm,
using nose-hoover thermostat, parinello-rahman pressure coupling, and
pme. Runnin the simulation in parallel is no problem (using 16 CPUs).
However when I want to run an almost identical molecu
Hi all
I have a ran a simulation of 64 molecules in a cubic box with side 6 nm,
using nose-hoover thermostat, parinello-rahman pressure coupling, and
pme. Runnin the simulation in parallel is no problem (using 16 CPUs).
However when I want to run an almost identical molecule using the exact
same c
Hello. I was wondering if anyone could explain how to convert delta G's from a
PMF (generated by umbrella sampling and WHAM) into standard state values? There
are some posts here on how to do this, but are too mathematical for me to
figure out. I also found the same problem when reading some pap
lloyd riggs wrote:
Hello again,
I am still working on gromacs sims on the side of wet lab work. In any case,
I am still at the same point as almost several weeks back.
I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro
file, with appropriate box (which can just be paste
Hello again,
I am still working on gromacs sims on the side of wet lab work. In any case, I
am still at the same point as almost several weeks back.
I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file,
with appropriate box (which can just be pasted at the top of the
Hi
I have run a lipid bilayer simulation, which has too much water in it and
too few lipids (small bilayer patch, ~ 80 waters per lipid). I have used
genconf to multiply the system in the xy direction to increase system size,
and then removed water which is z<8 angstroms and z>92 angstroms using v
Hi,
Does anyone have OPLS-AA topologies for ATP?
Thanks, Efrat--
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Hi,
Is there command in .mdp to adjust of frequency to write dg/dlamda to
dGdL.xvg file?
I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while
I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do?
thaks in advance,
Afsaneh Maleki
--
gmx-users mailing
Hi,
fcstep is only relevant for flexible constraints (hence the fc in the step).
It does not affect shells.
Berk
From: mstu...@slb.com
To: gmx-users@gromacs.org
Date: Tue, 22 Jun 2010 12:25:29 +0200
Subject: [gmx-users] fcstep value for shell particles
Dear all,
I am trying
Dear all,
I am trying to perform a simulation with polarizable model using Drude shell
particle approach. What should be the optimum value of fcstep if my shell
particle has zero mass? As far as I can understand, the default value for
fcstep is 0, but can't understand what does it mean from
I took initial 300 as equilibration,Now it seems fine.
Thank you ..
On Tue, Jun 22, 2010 at 9:21 AM, wrote:
> Take that replica on the left that shows a bimodal histogram. Now plot a
> time series of the displacement: x-axis = time and y-axis = displacement
> along reaction coord. Is it jumping
Hi,
I am trying to use g_sham to obtain free energy landscape from a simulation.
I can obtain the .xpm files but I want to know if there is any way of
obtaining the actual histogram (in a form of a ASCII matrix vith
numerical values) to use it in some other plotting program to draw
contour lines p
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