Du Jiangfeng (BIOCH) wrote:
Hi Guys,
I want to run a protein which contains some carboxylated residues into a
membrane. I have had to add a special residue into itp file since there is no
any description in normal itp for GLA residue. I admit some values I added for
GLA residue were ambiguous because I don't know the exact values.
After that, the system was blowing up when MD simulation with the following
warning:
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.029057, max 0.152326 (between atoms 81 and 82)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
43 44 37.0 0.0145 0.0148 0.0145
81 82 67.5 0.0078 0.0090 0.0078
89 90 34.7 0.0059 0.0060 0.0059
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056864, max 0.359219 (between atoms 81 and 82)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
43 44 35.6 0.0145 0.0147 0.0145
81 82 78.6 0.0078 0.0106 0.0078
89 90 34.3 0.0059 0.0060 0.0059
Apparently, some values about GLA residue are wrong in itp file. But I really
don't know how to set a correct value for it.
Without seeing what you actually did and knowing what force field you're using,
it's impossible to help. Missing parameters need to be derived in a manner
compatible with the original force field (no small task).
http://www.gromacs.org/Documentation/How-tos/Parameterization
-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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