[gmx-users] InflateGRO methodology deletion radius

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jun 19 06:39:19 CEST 2013

Do you mean the commands of inflateGRO controls the deletion radius?

 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?
Would you please give me a hint to go on?

Thanks for your suggestions in advance. Those are really kind of you.


----- 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>
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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list