It is a bit difficult to guess what is exactly happening. Your
starting structure
seem to be the problem, but your topology could also be partly
responsible.
One easy thing to do is the decrease your time step to 0.0001 which
would
decrease the chances that your system explodes.
Also
Hi,
If you have a liquid system (no off-diagonal elasticity), you should not use
full anistropic pressure coupling.
If you have a solid system (for instance a crystal), you will have an elastic
shear stress response
and you can determine and use off-diagonal compressibility values.
You
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Message: 2
Date: Thu, 19 Mar 2009 13:52:09 +0800
From: huifang liu huifangliu1...@gmail.com
Subject: [gmx-users] how to get the the force plot
Hello Berk and Justin. Thanks for the help.
In fact I was not using hardcore for electrostatic interactions
and also had a silly error in my topology. I fix everything and
now is working perfectly, without the giant peak near lambda = 0.
Bests
___
Eudes Eterno
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Message: 2
Date: Thu, 19 Mar 2009 13:52:09 +0800
From: huifang
Hello,I do have a crystal system. You refer to an initial guess. So if I
understand correctly, it is a trial and error, if I do not have any data, this
is what I can make out of. The part of the shear stress you are reffering I
think that it is from experimental values?
Now you say that :
Pawan Kumar wrote:
Hello Justin Sir,
Thanks for your reply.
I changed the dt value as per the suggestion.
But after 200 steps the same kind of warnings came like pressure
scaling more than 1% and 1-4 interactions and then it stopped after
writing few pdb files. Then I decreased the dt
Hello Justin Sir,
Thanks for your reply.
I changed the dt value as per the suggestion.
But after 200 steps the same kind of warnings came like pressure scaling
more than 1% and 1-4 interactions and then it stopped after writing few
pdb files. Then I decreased the dt value still lesser (0.1)
Hello Justin Sir,
Thanks for your reply.
I changed the dt value as per the suggestion.
But after 200 steps the same kind of warnings came like pressure scaling
more than 1% and 1-4 interactions and then it stopped after writing few
pdb files. Then I decreased the dt value still lesser (0.1)
Hi,
You will have to come up yourself with a reasonable guess.
If you have a hard crystal, I guess it would be close to the diagonal values.
Note that with PR coupling tau_p has to be large enough, something like 10 ps.
(note that in Gromacs 4.0 a bug has been corrected which scaled tau_p by
Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan
Thanks for your valuable suggestion and reply.
After inserting the protein in the bilayer using genbox I have minimized
the whole system without using any position restraints (i.e. define =
-DFLEXIBLE in em.mdp file). I used
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Hello,
I want to calculate the moments of inertia of a system of liquid crystals.
Using the tool g_gyrate I get 5 values. The three last values are called I1, I2
and I3. I suppose that they are Ixx, Iyy and Izz respectively. Is that correct?
What about the second column which is called Itot.
Antonia V. wrote:
Hello,
I want to calculate the moments of inertia of a system of liquid
crystals. Using the tool g_gyrate I get 5 values. The three last values
are called I1, I2 and I3. I suppose that they are Ixx, Iyy and Izz
respectively. Is that correct?
What about the second column
Hi, there are 3 questions I want to ask.
1. I run the md from the pdb file successfully and get a .trr trajectory
file. But when I load the .trr file in VMD, there is just 1 frame. I
have 1000 steps and want to have every step as a frame. How can I do this?
2. Since I do signal processing,
Date: Thu, 19 Mar 2009 11:51:51 +0800
From: xouy...@uvm.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Questions About Gromacs
Hi, there are 3 questions I want to ask.
1. I run the md from the pdb file successfully and get a .trr trajectory
file. But when I load the .trr file in
Hello,
I noticed that there is an inconsistency between the files ffG53a6nb.itp and
ffG53a6.rtp, and between the corresponding files in the ffG53a5 FF.
The atom type that is used for some CH2 atoms inside rings (e.g. CB CG CD in
Proline) is defined as CH2r type in the fG53a6nb.itp file (line
Hello Users
I have a question about defining an atom to be either hydrophobic or
hydrophilic.
The gromacs manual shows that the maximum charge of the hydrophobic atom is
0.2.
Does anyone know where this number is coming from?
Any good reasons or references?
Thank you in advance
Sunjoo
Xi Ouyang wrote:
Hi, there are 3 questions I want to ask.
1. I run the md from the pdb file successfully and get a .trr trajectory
file. But when I load the .trr file in VMD, there is just 1 frame. I
have 1000 steps and want to have every step as a frame. How can I do this?
Consult section
Hi all:
I wrote an e-mail many days ago about continuing run in Gromacs-4.0 with
check point file. But I can't solve this problem yet.
I run a simulation with
mpiexec -machinefile ./mf_24 -np 24 mdrun -v -append -cpt 5 -cpi
dppc_md_prev.cpt -cpo dppc_md.cpt -s dppc_md.tpr -o
xuji wrote:
Hi all:
I wrote an e-mail many days ago about continuing run in Gromacs-4.0 with
check point file. But I can't solve this problem yet.
I run a simulation with
mpiexec -machinefile ./mf_24 -np 24 mdrun -v -append -cpt 5 -cpi
dppc_md_prev.cpt -cpo
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