[gmx-users] About Doubt in Lipid protein Solvation

Justin Lemkul jalemkul at vt.edu
Wed Oct 31 17:11:46 CET 2012

On 10/31/12 11:45 AM, vidhya sankar wrote:
> Dear Justin Thank you For your Previous Kind Reply
>                                                                                I am following your Lipid-protein Tutorial  for My system   I  Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in the Tutorial
> Now the Problem in My solvation .
> I  Gave The Following Commands As Quoted in your Tutorial
> ./pdb2gmx_d  -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc
> ./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c
> ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3  -box 6 6 6
> ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top  -o emdppc.tpr -maxwarn 1
> ./trjconv_d -s emdppc.tpr -f dppc128n.gro  -o dppc128_whole.gro  -pbc  mol -ur compact
> ./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c
> cat 2KDQ_newbox.gro dppc128_whole.gro > system.gro
> ./genrestr_d  -f 2KDQ_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
> ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top  -o 2KDQDPPCem.tpr
> ./mdrun_d  -v -deffnm 2KDQDPPCem
> perl inflategro.pl 2KDQDPPCem.gro 0.95  DPPC 0 system_inflated1.gro 5 area1.dat
> I Repeated the inflate and EM  Until I have Attained  APL 66 (Experimental value 62)
> At the End of EMinimised .gro   file The Box vectors  Has been Increased form 6 6  6 6 to
> 20.57700  20.57700   6.00000

What do you mean "at the end of EM?"  Is this the first energy minimization of 
the inflated system, or the final minimization of the satisfactorily shrunken 
system?  If the latter, something is clearly wrong as it is impossible to have 
such a large x-y area with the quoted APL.

> As result Box Size Also Increase When I
> solvate   By mere Editing the Vanderwalls Radii  to 0.470,  then my
> system  is is solvated By 64495  Water molecules    How to Avoid this Problem  ?   This is too high  Where I have Committed Mistakes I need your Valuable Ideas  and Suggestions

I have no idea.  Your box size increases when you solvate?  That makes no sense. 
  Your description is not clear to me.



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


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