Thanks for your help, I followed you instruction, and I can get stable temperature after I remove the temperature coupling. In this case I used the flexible spc itp file. However if I use a rigid spc.itp, after remveing the temperature coupling, the system temperature is shooting up from 300K to thousands degree, the total energy is going up also instead of fluctuating. I attached both the itp files and grompp.mdp files. Let me know what could be wrong. It is really wired to me.
Thanks,
Cherry
Mark Abraham <[EMAIL PROTECTED]> wrote:
Cherry Y. Yates wrote:
> Dear GROMACS developers,
>
> I would like to do a SPC-water simulation without temperature coupling.
> I set tcouple to 300K and did Berenderson T-coupling first for 400 ps to
> equilibrate the system. Then I copy confout.gro to conf.gro, set tcoupl
> to no. However the Temperature of the later similation jumped from 300K
> to 520K immediately and fluctuate around 520K instead of 300K. I wonder
> (1) what could be wrong?
The .mdp file you attached has gen_vel = yes, which if used for the
second calculation will lead to regeneration of velocities and might
explain this behaviour. You will need to supply .trr and .edr files to
grompp for this second stage, of course.
> (2) how can I do a single simulation in which
> first 400 ps using some temperature coupling scheme to equilibrate the
> system, then do 100 ps without temperature coupling? I attached the
> grompp.mdp file.
You can't do this in a single simulation, however it's straightforward
to prepare your .mdp files in advance and have a script run a
grompp -f -c -p -o
mdrun -s
grompp -f -c -p -o -e -t
mdrun -s
sequence to deal with what you want to do.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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
Sponsored Link
Mortgage rates near historic lows: $150,000 loan as low as $579/mo. Intro-*Terms
spc_flxible.itp
Description: 2492990266-spc_flxible.itp
spc_rigid.itp
Description: 1737530030-spc_rigid.itp
grompp_ber.mdp
Description: 2875740139-grompp_ber.mdp
grompp_no_tc.mdp
Description: 3044091870-grompp_no_tc.mdp
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
