Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this and ask you if I have further doubts.
Is it fine if I use the perl code given in
wiki.gromacs.org/membrane-simulations
<http://wiki.gromacs.org/membrane-simulations> for solvation after the
genbox step to remove extra waters from the hydrophobic part of the
bilayer ?
You mean the C program or shell script at
http://wiki.gromacs.org/index.php/Membrane_Simulations? Yes, either of those
should be fine.
-Justin
Thanking you,
Yours sincerely,
Pawan
On Tue, Mar 31, 2009 at 5:31 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for all your suggestions.
Is it possible to use the lipid.itp file from Tieleman sir's
website in combination with GROMOS 96 force field without any
modification ?
If you want to use lipid.itp without any modification, you are
restricted to the ffgmx (deprecated!) force field. For
Gromos96-lipid.itp combination, simply remove the ";; parameters for
lipid-GROMOS interactions," as these nonbonded combinations are for
ffgmx only. Otherwise, the nonbonded interactions (which now have
consistent combination rules) should be generated correctly.
Is it fine if I use the Gromos/Berger force field combination
for the system I am using ?
That is a decision you will have to make based on a thorough
examination of the literature, and the benefits and criticisms of
these particular force field parameters.
I am sorry to ask this but can you please help me with some
information how to modify the lipid.itp file ?
That depends entirely upon what you want to do. If you want
Gromos/Berger, I've already told you. If you want OPLS/modified
Berger, search the archives for Chris Neale's posts on that topic.
-Justin
I will edit vdwradii.dat file as per your suggestion.
Thanking you,
Yours sincerely,
Pawan
On Tue, Mar 31, 2009 at 4:53 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
I have edited the lipid.itp file to add just one line
extra " H
atom from the opls_force_filed.itp " at the end of lipid
interactions data and that works fine.
I have done this after seeing the archives. It was given
either
I should change the file for sigma and epsilon values or else
just add this line.
I think I have done it correctly. If not please correct me.
No, that is incorrect. You need to add the additional atom
type as
well as convert C6/C12 to sigma/epsilon. Otherwise, the
calculated
nonbonded interactions are meaningless. Read instructions
carefully!
Force fields have to be internally self-consistent, so using the
parameters from OPLS with Berger lipids will give spurious
results.
The only proper combinations are Gromos/Berger or OPLS/converted
Berger.
I have removed the position restraints after the inflategro
procedure.
After that I did energy minimization using define =
-DFLEXIBLE.
I will change the temperature as per your suggestion.
I thought before solvating if I do position restraint
mdrun the
lipids will compact more surrounding the protein.
No, your system will probably explode due to unsatisfied charge
interactions and hydrogen bonds. There is a substantial
dipole in
each lipid headgroup that can repel the lipids away from each
other
if it is not shielded.
Thats the step when I got Lincs warnings and segmentation
fault.
Then I tried solvating the system using genbox step and
spc216.gro as the solvent.
But before doing the solvation step I copied the vdwradii.dat
file into the working directory and increased the value for
carbon to 0.5.
But the result of this was " Segmentation fault " again.
Can you
please tell me why I get the " Segmentation fault " here
in this
step.
The command used was : genbox -cp comp_em27.pdb -cs
spc216.gro
-o box.pdb -p topol.top
Using a 0.5-nm radius for carbon will cause problems of excess
memory consumption, or otherwise breaks the calculation. Use
something more along the lines of 0.35 or 0.375, and manually
delete
out any stray waters in the hydrophobic core.
-Justin
Thanking you,
Yours sincerely,
Pawan
On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
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>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>
<http://vt.edu>
<http://vt.edu> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list
gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
