Justin A. Lemkul wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
I have used force constants of 100000 in position restraint .itp files
for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
The mdp files are :
The .mdp files look reasonable enough, although I don't know why you are
applying position restraints during EM. If it is for InflateGRO, that
is fine, but once the system is assembled, you should remove the
position restraints from the protein to minimize the system more.
And are you sure you want 300K? DPPC will be in a gel phase at that
temperature. If you want a more realistic fluid-phase model, you'll
have to go above 315K (323K is common).
One thing I just noticed. You don't have solvent in your position-restrained
run? That could be a big problem if the lipid headgroups are strongly repelled
from one another. Add solvent before doing anything other than EM.
-Justin
*Topology file :*
; Include forcefield parameters
#include "ffoplsaa.itp"
#include "lipid.itp"
#include "dppc.itp"
This section should not work, as written. Have you modified lipid.itp
according to Chris Neale's half-epsilon double-pairlist method? If not,
what you've done makes no sense. The Berger lipid parameters
distributed through Tieleman's site are designed for use with the Gromos
force fields. They can be modified (search in the archives), but that
can also be a source of error. Users who have made mistakes in the
conversion have seen their systems explode.
-Justin
; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_C.itp"
;#ifdef POSRES
;#include "lipid_posre.itp"
;#endif
; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
PROTEIN IN DPPC BILAYER
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
Protein_C 1
DPPC 926
;SOL 23552
Please help with some suggestions.
Thanking you,
Yours sincerely,
Pawan
On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
I did the Inflategro procedure for the POPC bilayer generated
using genconf.
It took around 26 compressions for coming near the initial area
(just above it).
The minimization were all converged to Fmax < 1350.
If I decrease the Fmax less than this I am getting machine
precision.
But when I proceeded with the final compressed structure for pr
mdrun it gave lincs warnings and ended with segmentation fault.
As an alternative to this bilayer I used the DPPC bilayer
(pre-equilibrated) which is given in GMX-Benchmark distribution.
I carried out the same steps of Inflategro. I used the cutoff of
14 A in the inflation and compression step also.
In this case the the Steepest Descents converged to Fmax < 1000
in all the steps. The maximum force war never above 850.
But when I did position restraint mdrun with the last compressed
file I got Lincs warnings and Segementation fault after few
steps (30 - 40 steps).
Can you please help how to proceed ?
If the minimization procedure is adequately finishing, then the
problem comes from something you are doing. If you post your .mdp
file, we may be able to see if there are any obvious mistakes.
-Justin
Thanking you,
Yours sincerely,
Pawan
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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