Morteza Khabiri wrote:
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step, change coulomb type ,... but they did
not work ......
As MARK suggest me I try to minimize monomer separately but the monomers
itself also have high energy and it is not possible to minimize them...
OK, so simplify further to find the problem. Minimize just one half of a
monomer, etc. Consider writing a script to run the minimization to make
this process fast. Remember to look at the structures to identify
obvious problems.
Mark
I change the forcefield from olps to gromacs and minimization work. I did
several minimization by gromacs forcefiled and then I tried to minimized
the system by OPLS but again the system start exploiding...
Is there any idea that why the minimization work by gromacs but not work
with opls?????
finally I should simulate my system by opls and if I want to do it my
system still not minimized for OPLS....
I will apprecite if there will be some idea for my problem
thanks
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
