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<DIV><FONT face=Arial size=2>Hi all.<BR>I’m new to gromacs, and I would be glad
to get some advice from more experienced usres.<BR>I would like to estimate the
difference in free energy between two systems. <BR> First system (A)
consists of DPPC membrane, TM-protein and some Zn ions <BR>interacting
with the protein. Second (B) has the same elements but Zn ions <BR>are far
away from the protein (in the solvent). Is it possible to estimate
<BR>free energy difference between those two systems in gromacs?<BR>I thought
about using dummy atoms and slow-growth methods for free energy
calculations.<BR> During the simulation, Zn ions from system (A) would be
perturbated into dummy atoms<BR> (charge=0, mass = 0) and at the same time
equal number of dummy atoms in the solvent <BR>would be perturbated to Zn
atoms? Is it possible to achieve? <BR>For the beginning I
tried to estimate the difference in free energy between two systems.
<BR>1) first system consisted of two Cl- and one Zn2+ ions +
solvent<BR>2) second only solvent molecules <BR>During the 100 ps MD I
perturbated chare and mass of Cl and Zn <BR>ions to zero. The energy
values that I’ve obtained are wrong 960200,46.<BR> I’m new to gromacs so I
would appreciate your help a lot.<BR>Here are my input files (I’m using ffgmx
)</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>--------------md.mdp-------------</FONT></DIV>
<DIV><FONT face=Arial
size=2>pp
=
/lib/cpp<BR>define
=
-DFLEX_SPC<BR>constraints
= none<BR>integrator
=
md<BR>dt
=
0.001 <BR>nsteps
= 100000
<BR>nstxout
=
100000<BR>nstvout
=
100000<BR>nstfout
=
100000<BR>nstlog
=
100<BR>nstenergy
=
100<BR>nstxtcout
=
100<BR>nstlist
=
10<BR>ns_type
=
grid<BR>rlist
= 1.0<BR>free_energy = yes<BR>init_lambda = 0<BR>delta_lambda =
0.00001<BR>sc-alpha = 1.5<BR>sc-sigma = 0.3<BR>....</FONT></DIV>
<DIV><FONT face=Arial size=2>...</FONT></DIV>
<DIV><FONT face=Arial size=2>....</FONT></DIV>
<DIV><FONT face=Arial
size=2>---------------------------------------</FONT></DIV>
<DIV><FONT face=Arial size=2>--------ZN.itp-----------------------</FONT></DIV>
<DIV><FONT face=Arial size=2>[ moleculetype ]<BR>;
molname
nrexcl<BR>ZnB
1</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>[ atoms ]<BR>; id at type res
nr residu name at name cg nr
charge
typeB chargeB massB<BR>1
Zn 1
Zn
Zn 1
2 65.37000
Zn 0 0<BR></FONT></DIV>
<DIV><FONT face=Arial
size=2>---------------------------------------</FONT></DIV>
<DIV><FONT face=Arial size=2>-----------Cl.itp-----------------</FONT></DIV>
<DIV><FONT face=Arial size=2>[ moleculetype ]<BR>;
molname
nrexcl<BR>ClB
1</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>[ atoms ]<BR>; id at type res
nr residu name at name cg nr charge
typeB chargeB massB<BR>1
Cl 1
Cl
Cl 1
-1 35.45300 Cl
0 0<BR></DIV></FONT>
<DIV><FONT face=Arial>----------------------------</FONT></DIV>
<DIV><FONT face=Arial><BR> </DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>THANK YOU FOR HELP</FONT></DIV>
<DIV><FONT size=2>All the best.</FONT></DIV>
<DIV><FONT size=2>:)</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
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