Dr. Ramón Garduño-Juárez wrote:
Justin,
Again much obliged for your comments. They are most illustrative...
I would like to make a final note on the issue of these many e-mails...
I am sure that GROMACS is fast, but that fast?...
Yes. Your results prove it. With quality hardware, you get great performance.
For the sake of knowing that we are doing the right things, this is our
topol.top file in which we eliminated all POSRES for the Protein and
DMPC, not so for the WATER...
To what end, I do not know. One generally does not find much use in restraining
water while everything else moves, but syntactically, it is correct.
-------------
; Include forcefield parameters
#include "./gromos53a6_lipid.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"
; Include water topology
#include "./gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./gromos53a6_lipid.ff/ions.itp"
[ system ]
; Name
mod.pdb
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
----------------------
On Protein_chain_A there are 342 atoms
On Protein_chain_B there are 289 atoms
On Protein_chain_C there are 715 atoms
On DMPC there are 123 molecules of 46 atoms each
On SOL there are 3205 molecules of 3 atoms each
For a total of 16619 atoms
I know that this is a medium size system for which I was expecting
longer CPU time for a 20 ns MD run.
I know that there was no "error", which I meant is that I was surprised
by the outcome...
May be GROMACS is as fast as it is claimed...
Indeed.
-Justin
Cheers,
Ramon
El 04/04/2011 05:27 p.m., Justin A. Lemkul escribió:
Dr. Ramón Garduño-Juárez wrote:
Justin,
Thank you for your comments after finishing the MD production run for
up to 20 ns...
Since this step was over very quickly, now I have a simple question
¿How long, in human time, should a production run last?
There is no way to answer that. It depends on the hardware, number of
atoms, system load, application of any number of the Gromacs
algorithms, .mdp settings...
The production run was carried out in six processors Intel Xeon (R)
E5405 2.00 GHz. The last few lines of the md_0_1.log are:
-----------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 180685.417 180685.417 100.0
2d02h11:25
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 232.900 12.351 9.564 2.510
-----------------------------------------
Is this correct? In my opinion it should lasted much more longer...
Nope, Gromacs is just fast :)
Before reaching this point, this is an update of what we did...
First we eliminated the SOL_SOL group and the only special index
group was Protein_DMPC.
Since the NVT equilibration failed, we took option # 2 of the
"Advanced Troubleshooting", for the 1st phase of Equilibration.
After this step we proceeded with the equilibration phase 2 with a
1-ns NPT equilibration which ended fine.
Next, we proceeded with a 20 ns production run. Thus, the modified
lines of the .mpd file found in the tutorial page were:
nsteps = 10000000 ; 2 * 10000000 = 2000 ps (20 ns)
tc-grps = Protein DMPC SOL
comm-grps = Protein_DMPC SOL
With this instructions the 20 ns simulation took 2d02h11:25
I believe the "error" comes from the line
constrains = all-bonds which surely must be changed to
constrains = none or hbonds
Why do you say that? What error is occurring? You said your
simulations were running fine. You most certainly should not remove
constraints if you're sticking with a 2-fs timestep. The system will
be unstable without constraints. You might be able to get away with
hbonds, but certainly not "none."
-Justin
Looking forward to your comments...
Much obliged,
Ramon
--
========================================
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
