On 3/12/2011 5:15 PM, pragna lakshmi wrote:
I understood that the system has large velocities. Since simulation
has been stopped at Step 226040, time 452.08 (ps) can i conclude that
error is because of any invalid parameters in topology file generated
by server for ligand.
Such a conclusion w
I understood that the system has large velocities. Since simulation has
been stopped at Step 226040, time 452.08 (ps) can i conclude that error is
because of any invalid parameters in topology file generated by server for
ligand.
On Sat, Dec 3, 2011 at 11:19 AM, Mark Abraham wrote:
> On 3/12/201
On 3/12/2011 4:42 PM, pragna lakshmi wrote:
Thank u for reply. I did energy minimization and equilibration step.
It converged in 696 steps which is shown below.
Step= 692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03,
atom= 2099
Step= 693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax=
On 3/12/2011 4:42 PM, pragna lakshmi wrote:
Thank u for reply. I did energy minimization and equilibration step.
It converged in 696 steps which is shown below.
Step= 692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03,
atom= 2099
Step= 693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax=
Thank u for reply. I did energy minimization and equilibration step. It
converged in 696 steps which is shown below.
Step= 692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, atom=
2099
Step= 693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, atom=
2099
Step= 695, Dmax= 6.6e-
pragna lakshmi wrote:
Hi,
I am trying to run protein-ligand complex simulation. At the final
MD run step it is showing the following error. Can anybody tell me the
solution for this error?
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
There are hundreds
Hi,
I am trying to run protein-ligand complex simulation. At the final MD
run step it is showing the following error. Can anybody tell me the
solution for this error?
Step 105692, time 211.384 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002880, max 0.071917 (between a
Hello,
I am sorry, I did mean 5 nm box.
I did do the energy minimization but somehow overlooked the error message at
that stage.
Things seems to be working now.
Thanks for the time.
Shivangi
On Tue, Mar 29, 2011 at 2:06 PM, Justin A. Lemkul wrote:
>
>
> shivangi nangia wrote:
>
>> Hello gmx
shivangi nangia wrote:
Hello gmx-users,
I have a 5 ang box with equal number of water and methanol molecules
(1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system
is overall +2 charged.
If your box truly is 5 A (0.5 nm), grompp should have failed based on your
cutoffs.
Hello gmx-users,
I have a 5 ang box with equal number of water and methanol molecules (1800),
a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall
+2 charged.
I am trying to to do a NVT equilibration which runs into the following
error:
t = 0.000 ps: Water molecule startin
I believe that Justin was suggesting that you move in the opposite
direction than to delete some waters.
The number density for water should be about 32.5 waters per cubic
nanometer, meaning that you should have nearly 1E6 water molecules in
a cubic box with sides of 31 nm, and 1095 water m
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
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 create the file using genbox
(31.010 31.010 31.010). This is the energy minimization file I am using:
Surely a 31-nm cubic box is exces
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
nishap.pa...@utoronto.ca wrote:
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 t
quot;
Subject: Re: [gmx-users] Check for bad contacts and/or reduce the
timestep
To: "Gromacs Users' List"
Message-ID: <4b268d7b.1060...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
nishap.pa...@utoronto.ca wrote:
Steepest Descents converged
s warnings.
Could be possible that the same protocol works also in your case, else
follow Justin's advice.
Greetings Thomas
Message: 3
Date: Mon, 14 Dec 2009 14:09:47 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Check for bad contacts and/or reduce the
timestep
nishap.pa...@utoronto.ca wrote:
Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.7206969e+04
Maximum force = 2.0111207e+04 on atom 1217
Norm of force = 6.9283209e+02
I don't understand constraints I nee
- 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 tr
nishap.pa...@utoronto.ca wrote:
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
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
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