shivangi nangia wrote:
Hello Justin and everybody,
I created a system of charged polyhistdine, counter anions and just 1
DHB molecule is a box without making any change in the vdwradii.dat file.
This system does not energy minimize, it stops with the same message:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
What can be done to fix this problem?
Take some time to search the Gromacs website and the mailing list archive. You
would have undoubtedly found either this:
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
or the hundreds of other messages that post this message, which is neither a
problem, nor an error, per se.
The part of DHB itp file is:
[ moleculetype ]
; Name nrexcl
DHB 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DHB OAA 1 -0.567 15.9994
2 C 1 DHB CAH 1 1.135 12.0110
3 OM 1 DHB OAD 1 -0.568 15.9994
4 C 1 DHB CAK 2 -0.004 12.0110
5 CR1 1 DHB CAG 2 0.004 12.0110
6 HC 1 DHB HAG 2 0.033 1.0080
7 C 1 DHB CAI 2 0.141 12.0110
8 OA 1 DHB OAB 2 -0.179 15.9994
9 H 1 DHB HAB 2 0.005 1.0080
10 CR1 1 DHB CAE 3 0.000 12.0110
11 HC 1 DHB HAE 3 0.000 1.0080
12 CR1 1 DHB CAF 3 0.000 12.0110
13 HC 1 DHB HAF 3 0.000 1.0080
14 C 1 DHB CAJ 4 0.082 12.0110
15 OA 1 DHB OAC 4 -0.113 15.9994
16 H 1 DHB HAC 4 0.031 1.0080
This topology looks like complete junk. Earlier I provided you a link to PRODRG
tips and told you there was an article referenced there you should read. I
certainly hope you will do so. If you run a simulation with a lousy topology,
you'll get lousy results. Either the system will be unstable or the results
will be completely untrustworthy.
If I have the water/methanol or water:methanol in the system as the
solvent, the system runs fine.
Well, what's the solvent in the case of the unstable system? Just because some
other systems appear stable does not mean anything else will be.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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