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 value still lesser
(0.00001) and this time it continued with all the given steps but the
lipids' structure were distorted into small fragments.
If your system is not properly energy-minimized, there is no change in dt that
will help you. Ensure that your EM converged to reasonable values of Epot and
Fmax before continuing.
The other query I have is what should the optimal value for these
parameters for membrane proteins : rlist, rcoulomb, and rvdw. I have
used the value of 1 before.
These parameters depend upon the force field you are using. Read about the
parameter set, as well as modifications that may be made to it. Studies have
suggested that longer cut-off's should be used with membrane proteins. There is
no substitute for a thorough literature search before starting a project!
One last question is how to overcome the lincs warnings in position
restraint mdrun.
That will depend upon whether or not your system is properly constructed and
energy-minimized.
-Justin
Thanks in advance.
Thanking you,
Pawan
On Thu, Mar 19, 2009 at 5:01 PM,
Pawan Kumar wrote:
> Hi Xavier sir,
>
> Thanks for your valuable reply.
> How can I refine the non-bonded set-up ?
rlist, rcoulomb, rvdw as well as coulombtype. *Never* use cut-off
electrostatics for a membrane system (or really any other, for that
matter).
Your results will be far less accurate than with PME (this is in the
literature).
> And where can I specify the time step to 0.0001 ?
dt (read the manual).
-Justin
> I am new to gromacs.
> Sorry to ask such questions.
>
> Thanking you,
> Pawan
>
>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
