[gmx-users] soft-core and coulomb transformation

[David Mobley]

Bharat,

Your values for the first set of calculations (the forward case?)
below look really weird. I suspect you have something messed up in
those runs. Have you checked that your define statements worked
properly, and checked your run input files? In particular, your
<dv/dlambda> is staying almost constant as a function of lambda, which
shouldn't be the case. Check the headers of your log files, perhaps,
and make sure lambda is set to what you think it should be, and make
sure your define statement for forward and reverse is really working
properly.

I'll do some more poking around myself.

Also, take a look at the charge groups in your topology file; I'm not
too up on how charge groups are supposed to be used, but I do remember
that when I usually set up proteins using pdb2gmx, I usually get
roughly one charge group per atom, and you have one charge group per
residue for a couple of your residues, but the middle residue is split
into three. Not sure how you decided to do that but it looks weird --
may want to look at the documentation here.

David


On Nov 9, 2007 11:27 PM, bharat v. adkar <bharat at sscu.iisc.ernet.in> wrote:
>
> hi,
>   i am pasting the xmgrace file for the both forward and reverse
> transformation of charge modification for Ala->Gly mutation.
>
> The simulations are performed in water. when you open the file with
> xmgrace, you can clearly see the behaviour what i was describing in
> previous mails.
>
> bharat
>
>
>
>
> #
> # Grace project file
> #
> @version 50120
> @map color 11 to (255,0,0), "red"
> @with g0
> @    world -0.05, -5.45, 1.05, 4.45
> @    view 0.150000, 0.150000, 1.150000, 0.850000
> @    title "charge transformation"
> @    subtitle "without soft-core potentials"
> @    xaxis  on
> @    xaxis  label "\xl\f{}"
> @    xaxis  tick on
> @    xaxis  tick major 0.2
> @    xaxis  tick minor ticks 1
> @    xaxis  ticklabel on
> @    yaxis  on
> @    yaxis  label "dG/d\xl\f{} (kJ\#{b7}mol\S-1\N\#{b7}\xl\f{}\S-1\N)"
> @    yaxis  tick on
> @    yaxis  tick major 1
> @    yaxis  tick minor ticks 1
> @    yaxis  ticklabel on
> @    legend on
> @    legend 0.5, 0.8
> @    legend box pattern 0
> @    s0 type xydy
> @    s0 errorbar on
> @    s0 comment "FWD/coul_fwd_dgdl"
> @    s0 legend  "fwd [(Ace-Ala-Nac) --> (Ace-Gly-Nac)]"
> @g1 on
> @g1 hidden false
> @g1 type XY
> @g1 stacked false
> @g1 bar hgap 0.000000
> @g1 fixedpoint off
> @g1 fixedpoint type 0
> @g1 fixedpoint xy 0.000000, 0.000000
> @g1 fixedpoint format general general
> @g1 fixedpoint prec 6, 6
> @with g1
> @    world -0.05, -4.45, 1.05, 5.45
> @    view 0.150000, 0.150000, 1.150000, 0.850000
> @    xaxes invert on
> @    yaxes invert on
> @    xaxis  on
> @    xaxis  tick on
> @    xaxis  tick major 0.2
> @    xaxis  tick minor ticks 1
> @    xaxis  ticklabel place opposite
> @    xaxis  ticklabel color 11
> @    yaxis  on
> @    yaxis  tick on
> @    yaxis  tick major 1
> @    yaxis  tick minor ticks 1
> @    yaxis  ticklabel place opposite
> @    yaxis  ticklabel color 11
> @    legend on
> @    legend 0.5, 0.75
> @    legend box pattern 0
> @    s0 type xydy
> @    s0 line color 11
> @    s0 errorbar on
> @    s0 errorbar color 11
> @    s0 comment "REV/coul_rev_dgdl"
> @    s0 legend  "rev [(Ace-Gly-Nac) --> (Ace-Ala-Nac)]"
> @target G0.S0
> @type xydy
> 0.00 -2.203320 0.055352
> 0.05 -2.299345 0.0520252
> 0.10 -2.358355 0.145189
> 0.15 -2.318708 0.108821
> 0.25 -2.506092 0.055204
> 0.35 -2.201419 0.0590116
> 0.45 -2.484940 0.0969871
> 0.50 -2.433880 0.0532859
> 0.55 -2.462887 0.0775993
> 0.65 -2.619397 0.0606133
> 0.75 -2.622916 0.0757515
> 0.85 -2.517759 0.0644187
> 0.90 -2.636431 0.0590214
> 0.95 -2.599439 0.10389
> 1.00 -2.563080 0.0581629
> &
> @target G1.S0
> @type xydy
> 0.00 4.627166 0.0879965
> 0.05 4.118060 0.0790556
> 0.10 3.916284 0.0833586
> 0.15 3.588531 0.0804413
> 0.25 2.666605 0.0928452
> 0.35 1.823581 0.0706488
> 0.45 1.047328 0.0957733
> 0.50 0.837857 0.0728831
> 0.55 0.529029 0.0765816
> 0.65 -0.281202 0.0716938
> 0.75 -0.995985 0.0706986
> 0.85 -1.947576 0.0761678
> 0.90 -2.328663 0.0707552
> 0.95 -2.589109 0.0834396
> 1.00 -3.052700 0.0640444
> &
>
>
> --
>
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