Pawan Kumar wrote:
Hello Sir,
Can you please tell me how to couple ions with SOL ?
Is there any command in gromacs to do that ?
You need to define a group with SOL and the ions in an index file. This
is uses as input to grompp so that it can make sense of the same group
name when used in the
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Sorry for the inconvenience about the .mdp file.
The mdp file used for the final run is
*_
final.mdp file_*_
_title = Protein in POPC bilayer
cpp = /usr/bin/cpp
constraints = all-bonds
constraint-al
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
1. Were there gaps between the water and lipid headgroups? If so,
the lipids may be pulling towards the solvent. Restrain the lipids
and run an equilibration for a longer time.
Gap was there when I used a value of 0.
Respected Sir,
Greetings from Pawan.
Before inserting the protein the bilayer was alright as I took the
equilibrated bilayer from Dr. Tieleman's website.
I have done the position restraint mdrun by restraining the protein only. In
this case also the lipids pull apart.
Thanking you,
Pawan
On Mon,
There is nothing wrong with the number of steps and the step size of 2 fs. Can
you attach/send the coordinates of your system after position restraint MD ?
What about your bilayer before inserting the protein ? Does it move apart
during MD ?
Definetly you should perform another position restra
Apparently the final mdrun has not worked successfully. It would be interesting
to see what the system looks like after the position restraint mdrun.
Andreas
>>>
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Pawan Kumar
Sent: 06 April 2009 07:47
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for all your suggestions.
Is it possible to use the lipid.itp file from Tieleman sir's website in
combination with GROMOS 96 force field without any modification ?
If you want to use lipid.itp without any modification, you are r
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 vanderwaa
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 vanderwaal's distance parameter (
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.
fangliu1...@gmail.com>
Fax: (86-21)54237264
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Message: 3
Dat
. But i don't know how
> to get the force plot. Is there some one can give me a suggestion?
> Thank you very much.
>
> Huifang
>
> --
> Huifang Liu (Ph.D. Student)
> School of Pharmacy
> Fudan University
>
> 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
> Shanghai, China, 200032 Cell
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 tr
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