Dear Mark:
Thanks for your suggestions. I did equilibration for about 500ps but
still there is energy fluctuation exist (as give below). Is this deviation
is acceptable for NVE ensemble or still i need to equilibrate the system for
some more picosecond.
Energy
Mark Abraham skrev:
On 31/03/2010 2:51 PM, Ramachandran G wrote:
Dear gromacs users:
I am using following mdp file as input for simulating the
system with NVE ensemble. But when i check the 'Total energy',
it doesn't seems to remain constant and keep decreasing. I am also
Thus, you
Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each
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Hi,
What does this mean?
Program mdrun, VERSION 4.0.7
Source code file: constr.c, line: 243
Software inconsistency error:
constrain called for forces while not doing energy minimization, can not
do this while the LINCS and SETTLE constraint connection matrices are
mass weighted
Below is part
Hi,
You can not use constraints with normal modes.
A user should not see software inconsistency errors,
we should add a check for constraints with nm.
Berk
From: zhao0...@ntu.edu.sg
To: gmx-users@gromacs.org
Date: Thu, 1 Apr 2010 17:28:47 +0800
Subject: [gmx-users] the LINCS and SETTLE
Message: 5
Date: Thu, 01 Apr 2010 16:30:44 +1100
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] custom forcefields or a new forcefields
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4bb42f84.9050...@anu.edu.au
Content-Type: text/plain;
On 1/04/2010 9:08 PM, DreamCatcher wrote:
Message: 5
Date: Thu, 01 Apr 2010 16:30:44 +1100
From: Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
Subject: Re: [gmx-users] custom forcefields or a new forcefields
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi
Basically you can provide a file in which you calculate the values of your
potential function for different values of r. You will have to write a
small program to create the table file yourself I think. The details of
what should be in it are described in section 6.7.2 of the manual but
Oh almost forgot you also have to put
vdw-type = user
in the mdp file. As this tell gromacs to read in the tables.
Gareth
On Thu, Apr 1, 2010 at 3:25 PM, Gareth Tribello
gareth.tribe...@gmail.comwrote:
Hi
Basically you can provide a file in which you calculate the values of your
grivet wrote:
Le mardi 30 mars 2010 à 12:26 -0400, Justin A. Lemkul a écrit :
Having cleared the first hurdle, I ran mdrun for steepest descent (5832
molecules). The program stopped after 2067 steps, with maximum force =
1.58E02 on atom 4870. How important is that warning?
What warning?
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
Title: how to get averaged coordinates for a residue in a time interval?
Dear all,
How to get the averaged coordinates for a short time range say, 10 ps? which utility should be used?
r. q.
--
gmx-users mailing listgmx-users@gromacs.org
Wu Rongqin wrote:
Dear all,
How to get the averaged coordinates for a short time range say, 10 ps?
which utility should be used?
g_traj to extract the coordinates, g_analyze to do averaging.
-Justin
r. q.
--
Justin A. Lemkul
Ph.D. Candidate
Greetings,
My system consists of large non-polar spheres in tip4p water, and the user
potential option is implemented to define vdw interactions. Because the radius
of the sphere is on the order of 1 nm, I am using a cutoff of 1.9 nm for the vdw
portion. I would like to save on computational
Hi Nisha,I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is
Well, you could also use g_rmsf with -b and -e, and a suitable index file...
Cheers,
Tsjerk
On Thu, Apr 1, 2010 at 6:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Wu Rongqin wrote:
Dear all,
How to get the averaged coordinates for a short time range say, 10 ps?
which utility should be
Hello all,
Please, can someone let me know why there are X's in the [dihedraltypes]
section of the ffcharmm27bon.itp force field and what they actually stand
for? Could they be replaced with actual atoms or no?
I appreciate your replies.
Lum
--
gmx-users mailing listgmx-users@gromacs.org
On 2/04/2010 4:50 AM, Lum Nforbi wrote:
Hello all,
Please, can someone let me know why there are X's in the
[dihedraltypes] section of the ffcharmm27bon.itp force field and what
they actually stand for? Could they be replaced with actual atoms or no?
I appreciate your replies.
That's a
On 2/04/2010 3:56 AM, Robin C. Underwood wrote:
Greetings,
My system consists of large non-polar spheres in tip4p water, and the user
potential option is implemented to define vdw interactions. Because the radius
of the sphere is on the order of 1 nm, I am using a cutoff of 1.9 nm for the vdw
Hello all,
I have built a parameter file for the AOT surfactant molecule and tried
to minimize the energy of a mixture of several of this molecule and water
molecules but I have the warnings at the bottom part of this mail. Gromacs
basically goes through all the lines of parameters starting
Dear All,
I am running MD simulation with TIP4P water and OPLS force field in NVT and
NVE. I have noticed a continuous energy increase in both NVE and NVT
simulations when i freeze a selected portion of my system. Recently i had
problem with temperature coupling, Berk has sent me a file which has
Justin,
I appreciate your reply. Actually, I have read through the section of
building parameter files in chap. 5 several times. The only reason for using
atom types instead of numbers is because that is the way they are
represented in the ffcharmmbon.itp and ffcharmmnb.itp files. Numbers are
On 2/04/2010 3:07 PM, Lum Nforbi wrote:
Justin,
I appreciate your reply. Actually, I have read through the section
of building parameter files in chap. 5 several times. The only reason
for using atom types instead of numbers is because that is the way they
are represented in the
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