James Starlight wrote:
Justin,thanks!
1) For example for the situation presented in manual for 2 groups with 3
and 4 points the time enty should be
annealing_time = 0 3 6 0 2 4 6
from this I've understood that 0 value is the start of timer for each
group and subsequent values are the actual time in the ps, havennt it ?
Yes.
For example I'd like to perform nvt simulation ( with overal time 100ps)
for three different groups in 5 equal steps. So does annealing options
must be
annealing = single single single
annealing_npoints = 5 5 5
annealing_time = 0 25 50 75 100 0 25 50 75 100 0 25 50 75 100
annealing_temp = 300 310 320 330 340 350 300 310 320 330 340 350 300 310
320 330 340 350
# this means that for each group temperature increase on 10K on each
step and there are 5 steps for each grou ( equal to npoints)
I don't understand why 5 steps are necessary. You're doing a linear increase
from 300K to 350K for all groups over 100 ps. All you need is:
annealing = single single single
annealing_npoints = 2 2 2
annealing time = 300 350 300 350 300 350
Does this ecxample correct or there are some connection between that
values for diffent groups ?
2) How I can couple this annealing options with the *gen_temp* values
wich as I understood must also differs on the each step ? OR should I
use some averaged gen_temp?
The value of gen_temp is only used for initial velocity generation, so in your
case it should still be set to 300. After that, it is irrelevant. Do you mean
ref_t? In this case, the annealing temperature values override ref_t, so it
doesn't matter.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
