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
--
========================================
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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