[gmx-users] InflateGRO methodology deletion radius

[Shima Arasteh]

Do you mean another published paper rather than published one in Methods Journal? Another one which explains the algorithm?


 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, June 19, 2013 3:45 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius



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 <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at 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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