On 10/7/12 12:24 AM, vidhya sankar wrote:
Dear justin Thank you for your previous reply
I am
running NPT Equlibration at 20 ps with dt 0.0002 in 100000 steps Without
usage of Lincs Algorithm and its related parameters it runs Successfully .
But When I Increase dt from 0.0002 to 0.002 then I have got error as follows
in grompp
WARNING 1 [file 2KDQTR.top, line 71]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
an estimated oscillational period of 1.0e-02 ps, which is less than 5
times the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
One cannot arbitrarily increase the timestep to such a value without using
constraints. The relationship between timestep and bond vibrational frequencies
is discussed in every major simulation textbook.
Then I have used the Lincs Algorithm and its related parameter Then I have got
Error during Mdrun as follows I saw there Are Plenty Of discussion in Mailing
list But I am Not Able to come to conclusion
relative constraint deviation after LINCS:
rms 0.015272, max 0.577865 (between atoms 120 and 122)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Wrote pdb files with previous and current coordinates
129 131 39.1 0.1475 0.1664 0.1330
129 130 37.8 0.1191 0.1243 0.1230
125 126 38.5 0.1738 0.1508 0.1530
124 129 103.2 0.0962 0.9157 0.1530
124 125 124.3 0.1725 0.8648 0.1530
122 124 169.9 0.4717 2.5621 0.1470
122 123 168.0 0.2655 3.1890 0.1000
120 122 176.3 0.5957 7.3414 0.1330
120 121 172.8 0.5550 6.4843 0.1230
What does the Above Fact Indicates I mean the Problem is in Topology or in MD
Parameter file ?
Either, or both. It's impossible to say without a more thorough description of
your system, what you have done to minimize and equilibrate it, and what you're
trying to do. Basically everything you would be advised is already described here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-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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