Steve Vivian wrote:
On 03/12/2011 01:36 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
On 03/12/2011 12:51 PM, Justin A. Lemkul wrote:
Getting hard to follow, so I put my new comments in blue.
Output from Energy Minimization
Steepest Descents converged to Fmax < 1000 in 1814 steps
Potential Energy = -3.81270276926664e+05
Maximum force = 9.38712770623942e+02 on atom 2292
Norm of force = 2.88274347161761e+01
Steve Vivian wrote:
Based on a preliminary test using multiple threads, the issue is not
resolved.
This leads me to believe that my Unit Cell is not built properly.
Below is the procedure used to build the unit cell. I have
reviewed it many
times, but I would appreciate any input regarding potential
improvements,
specifically on the line using trjconv in the EM/Shrink loop.
Safe up to here, (I hope)...
cat KALP_newbox.gro dppc128_whole.gro > system.gro
update minim.mdp
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif
Create Strong Position Restraint for protein
genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000
100000
Scale Lipid positions by a factor of 4
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
Begin loop of repeated Energy Minimizations and Shrinking (repeat
loop approximately 25 times until area is approx 71 Ang sq)
Begin LOOP (from n=1 to n = 26)
grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr
mdrun -v -deffnm em_n
trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur
compact
perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5
One problem here: you start the loop every time with system_inf_n?
What is system_inf_n? It seems that you should start one (non-loop)
shrink and then process the subsequent shrinking steps from there.
At the end of the loop, you write to sys_shr_1.gro, which then never
gets used again.
-Justin
Put my comments in blue to make it easier to read.
I apologize for the poor description here. The first loop begins with
the System_inflate.gro file created in the earlier process. The rest
of the first loop is shown.
At the beginning of the second loop, the input file is
system_shrink_1.gro, which was the output file at the end of loop 1.
Proceed through the loop, updating the n from 1 to 2 in each step.
Output file is system_shrink_2.gro.
Input file for loop 3 is system_shrink_3.gro, ....
....Output from loop 26 is system_shrink_26.gro and output on screen
provides information on updated Lipid area which has achieved target
value.
Then proceed to add water (after changing vdw radius of C atoms)
Add ions
EM again
Then Equilibrate.
Output from Energy Minimization (after addition of water and ions)
Steepest Descents converged to Fmax < 1000 in 1814 steps
Potential Energy = -3.81270276926664e+05
Maximum force = 9.38712770623942e+02 on atom 2292
Norm of force = 2.88274347161761e+01
This output indicates to me that the system is completely reasonable.
If you send me your .gro and .top (off-list), I will try to debug and
report back if I can find anything.
To confirm, you are using Gromacs 4.5.3? What version of FFTW? What
hardware? What compilers were used for the installation?
-Justin
Using Gromacs 4.5.3 and FFTW 3.2.2 both compiled for double precision.
It has been a while since I compiled so I'm not exactly sure, but I
recall updating gcc and gfortran during the process.
Hardware, what type of specifics are you looking for? # of processors
and speed?
Attached are current Energy Minimized file and topology file.
Hardware and compiler specs are unnecessary. The problem is the coordinate file
itself. Look at it in your favorite visualization program and you will see that
the lipid headgroups are completely collapsed in on one another. I don't know
how or why this happened. If you're using the DPPC topology from Tieleman and
the .mdp files given in the tutorial, I see no reason for this totally unstable
configuration. I have never used double precision (and it is not necessary for
standard MD, and only serves to slow your runs down), so it would be interesting
to see if the problem is a result of double vs. single precision. I can
successfully re-minimize the coordinate file you sent me using single precision:
Steepest Descents converged to Fmax < 1000 in 335 steps
Potential Energy = -6.3605750e+04
Maximum force = 7.1865680e+02 on atom 115
Norm of force = 3.9649860e+01
For now, I would suggest you test the precision issue. Install Gromacs again
(making note of your compiler versions, because this is important to know!) in
single precision and try to re-minimize the system and proceed. No need to
completely re-build it, as you should be able to just run a new EM on your
existing system like I did.
-Justin
Steve.
ar_shr1.dat
End LOOP
Add water Add ions
Re-run EM
Equilibrate (and watch it all explode)
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Thursday, March 10, 2011 12:56 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0
Segmentation
Fault
Steve Vivian wrote:
On 03/08/2011 10:23 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
New to Gromacs.
Worked my way through the tutorial with relatively few issues
until the Equilibration stage. My system blows up!!
Returned to the Topology stage and rebuilt my system ensuring
that I followed the procedure correctly for the InflateGro
process. It appears to be correct, reasonable lipid area, no
water inside my bilayer, vmd shows a structure which appears
normal (although I am new to this). There are voids between
bilayer and water molecules, but this is to be expected, correct?
Energy Minimization repeatedly produces results within the
expected range.
Again system blows up at equilibration, step 0 segmentation
fault. Regardless of whether I attempt the NVT or Anneal_Npt
process (using the provided mdp files, including the updates for
restraints on the protein and the lipid molecules).
I have attempted many variations of the nvt.mdp and
anneal_npt.mdp files hoping to resolve my issue, but with no
success. I will post the log information from the nvt.mdp file
included in the tutorial.
Started mdrun on node 0 Tue Mar 8 15:42:35 2011
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 9 x 9 cells
Energies (kJ/mol)
G96Angle Proper Dih. Improper
Dih. LJ-14 Coulomb-14
8.52380e+01 6.88116e+01 2.23939e+01
-3.03546e+01 2.71260e+03
LJ (SR) Disper. corr. Coulomb
(SR) Coul. recip. Position Rest.
1.49883e+04 -1.42684e+03 -2.78329e+05
-1.58540e+05 2.57100e+00
Potential Kinetic En. Total
Energy Conserved En. Temperature
-4.20446e+05 *1.41436e+14 1.41436e+14
1.41436e+14 1.23343e+12*
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.56331e+02 5.05645e+12 1.18070e+01
As you can see the Potential Energy is reasonable, but the
Kinetic Energy and Temperature seem unrealistic.
I am hoping that this is enough information for a more
experienced Gromacs user to provide guidance. Note: that I have
tried all of the suggestions that I read on the mailing list and
in the "blowing up" section of the manual, specifically:
-reduced time steps in Equilibration Stages
-reduced Fmax during EM stage (down as low as 100kJ which did
not help)
-modified neighbours list parameters
Any help is appreciated. I can attach and forward any further
information as required, please let me know.
Which Gromacs version are you using? It looks like you're
running in serial, is that correct? Otherwise, please provide
your mdrun command line. If you're using version 4.5.3 in
serial, I have identified a very problematic bug that seems to
affect a wide variety of systems that could be related:
Yes I am currently using Gromacs 4.5.3 in serial.
http://redmine.gromacs.org/issues/715
I have seen even the most robust tutorial systems fail as well,
as some new lab members experienced the same problem. The
workaround is to run in parallel.
If I understand you correctly, the recommended workaround is to
re-configure gromacs 4.5.3 with mpi enabled and complete the
Equilibration and Production simulation in parallel.
Strictly speaking, an external MPI library is no longer required.
Gromacs
now builds with internal threading support (as long as your
hardware and
compilers support such features). In fact, thread support builds
by default if
possible, so if your mdrun has an -nt flag, you don't need to do
anything else except
use "mdrun -nt (number of threads)" when running your command.
Do you have a recommendation for which mpi library to install (lam
mpi seems to be referenced in other articles on the mailing list)?
I've had good luck with OpenMPI in the past, but this is not strictly
necessary in all cases.
Are there documented installation procedures for this process
(upgrading to gromacs with mpi enabled)?
http://www.gromacs.org/Downloads/Installation_Instructions#Using_MPI
-Justin
Thanks for your assistance.
Steve.
-Justin
Regards,
Steve Vivian.
sviv...@uwo.ca
--
========================================
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
