Aditi Borkar wrote:
Thanx Justin.
I had tried that too. Using both parameters I get the same outcome. I
notice that increasing the emtol to 2000 (that effectively reduces the
number of steps my system undergoes before converging) retains most of
the structure. Should I change the dielectric constant of the solvent
because my system is highly charged ( -744 e). The topology parameters
from ASP side chain that I used are as follows:
I would take a step back and consider whether or not this model system is even
valid. A 1M solution of acetic acid would have a pH of roughly 2.4, meaning
that most of the molecules would be protonated; a 9M solution would probably be
at pH close to 0, meaning that having 744 negatively-charged molecules of
acetate probably does not come close to modeling reality.
If anything, you should probably be working with a net neutral system, since you
are probably experiencing a significant amount of charge repulsion in the
system. But strongly consider whether or not this model is appropriate.
-Justin
[ moleculetype ]
; Name nrexcl
ACA 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 CH3 1 ACA CB 1 0 15.035 ; qtot 0
2 C 1 ACA CA 2 0.27 12.011
; qtot 0.27
3 OM 1 ACA OD1 2 -0.635 15.9994
; qtot -0.365
4 OM 1 ACA OD2 2 -0.635 15.9994 ; qtot -1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_26
2 3 2 gb_5
2 4 2 gb_5
[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 2 ga_21
1 2 4 2 ga_21
3 2 4 2 ga_37
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
1 4 3 2 2 gi_1
-Aditi Borkar,
TIFR,
Mumbai, India
On Sat, Sep 12, 2009 at 5:35 PM, Justin A. Lemkul <[email protected]> wrote:
Aditi Borkar wrote:
Dear All,
Hello!
I am simulating a protein in a box of 9M acetic acid. I have obtained
the coordinates and gromacs topology for AcOH from PRODRG. The AcOH
has net -1 charge and the topology file is as follows:
PRODRG topologies generally produce unsatisfactory charges. For acetic
acid, I would use the same charges found in an ASP side chain as a starting
point. You will note that your topology differs greatly from an ASP side
chain in any of the Gromos96 force fields.
[ moleculetype ]
; Name nrexcl
ACA 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 ACA CAA 1 0.056 15.0350
2 C 1 ACA CAD 1 0.393 12.0110
3 OM 1 ACA OAC 1 -0.725 15.9994
4 OM 1 ACA OAB 1 -0.724 15.9994
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAA CAD
2 3 1 0.125 418400.0 0.125 418400.0 ; CAD OAC
2 4 1 0.125 418400.0 0.125 418400.0 ; CAD OAB
[ pairs ]
; ai aj fu c0, c1, ...
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 120.0 418.4 120.0 418.4 ; CAA CAD
OAC
1 2 4 1 120.0 418.4 120.0 418.4 ; CAA CAD
OAB
3 2 4 1 126.0 502.1 126.0 502.1 ; OAC CAD
OAB
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 4 3 2 0.0 1673.6 0.0 1673.6 ; imp CAD
CAA OAB OAC
When I had tried taking uncharged AcOH, during equilibration, the
water and AcOH were completely segregating into two layers (like a
biphasic system).
My problem arises when I perform energy mimization on my solvated
protein. With 300 steps of EM (emtol 1000 and emstep .01) the EM
doesn't converge and more distrurbingly within these few steps, the
secondary structure of my protein is completely lost. This problem
does not occur when I do EM in box containing protein and pure water.
The Fmax is displayed onto 2 TRP residues.
It is strange that this degree of change is occurring during EM. But I
wouldn't try anything else until you're sure you are starting with
reasonable parameters (see above).
-Justin
My em.mdp file is as follows:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 300
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
Please help!
Thank you!
-Aditi Borkar,
Tata Institute of Fundamental Research,
Mumbai,
India.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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