On 6/19/13 12:39 AM, Shima Arasteh wrote:
Do you mean the commands of inflateGRO controls the deletion radius?
Yes, that's its purpose. There is a published paper about its algorithm; I
would suggest you read and understand it.
The command which I use is what I got from tutorial:
#perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat
Am I supposed to decrease 5 as deletion radius?
The value of 5 is a grid spacing for the InflateGRO APL measurement. The
deletion radius is zero, which is correct for shrinking because you don't want
to continue deleting lipids, or you will have no membrane left!
Would you please give me a hint to go on?
If these concepts are not intuitive, you should absolutely stop and read the
paper for InflateGRO and watch the demonstration video that is posted online.
-Justin
Thanks for your suggestions in advance. Those are really kind of you.
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@gromacs.org>
Cc:
Sent: Saturday, June 15, 2013 4:18 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius
On 6/15/13 3:56 AM, Shima Arasteh wrote:
> Hi,
>
> In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack
the lipids, I need to follow the iteration while the cutoff value changed to 0.
> I' d like to know what settings of EM.mdp file are suggested to get the best
results of doing shrinking steps?
> When I set the settings as follow, the lipids interfere the peptide however
the APL doesn't get the experimental value. So the configuration is not ideal to
get through the equilibrium steps.
>
> define = -DPOSRES
> integrator = steep ; Algorithm (steep = steepest descent
minimization)
> emtol = 100.0 ; Stop minimization when the maximum force < 100.0
kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to
perform
> ; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and
long range forces
> ns_type = grid ; Method to determine neighbor list (simple,
grid)
> rlist = 0.4 ; Cut-off for making neighbor list (short range forces)
> rlistlong = 6.0
> coulombtype = PME ; Treatment of long range electrostatic
interactions
> rcoulomb = 0.4 ; Short-range electrostatic cut-off
> rvdw = 0.4 ; Short-range Van der Waals cut-off
> vdwtype = switch
> rvdw_switch = 0.2
> pbc = xyz ; Periodic Boundary Conditions
>
>
>
> Now, I am wondering if such a settings will serve a proper deletion radius?
>
No. These settings make no sense to me whatsoever. Don't be confused by the
"cutoff" used by InflateGRO and the cutoff values used in the .mdp file.
InflateGRO uses a search radius to delete lipids, which is specified on the
command line. The cutoff values for the EM and MD runs are dictated by the
force field you are using and are in no way connected to lipid deletion.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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