On 7/8/12 6:57 AM, James Starlight wrote:
Justin,
unfortunately my last system have also been crashed after 35ns of
simulation with the links warnings accompanied by the error
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
This time I've devided all functional groups of my ADENOSINE ligand
into separate charge groups in topol.itp.
Note that these charges are not the same as the adenosine moiety of ATP, which
is standard in the Gromos96 force fields. Perhaps you should re-evaluate some
charges (see aminoacids.rtp for the existing ATP implementation).
; nr type resnr resid atom cgnr charge mass total_charge
1 NT 1 ADN N6 1 -0.844 14.0067
2 H 1 ADN H11 1 0.422 1.0080
3 H 1 ADN H12 1 0.422 1.0080 ; 0.000
4 C 1 ADN C8 2 0.097 12.0110
5 HC 1 ADN H01 2 0.177 1.0080
6 NR 1 ADN N3 2 -0.642 14.0067
7 C 1 ADN C4 2 0.175 12.0110
8 C 1 ADN C5 2 0.092 12.0110
9 NR 1 ADN N7 2 -0.556 14.0067
10 C 1 ADN C6 2 0.657 12.0110 ; 0.000
11 C 1 ADN C5' 3 -0.677 12.0110
12 C 1 ADN C4' 3 0.834 12.0110
13 OE 1 ADN O4' 3 -0.248 15.9994
14 C 1 ADN C1' 3 -0.558 12.0110
15 C 1 ADN C2' 4 0.603 12.0110
16 C 1 ADN C3' 5 -0.212 12.0110
17 NR 1 ADN N9 3 0.415 14.0067
18 OA 1 ADN O2' 4 -0.606 15.9994
19 H 1 ADN H08 4 0.482 1.0080
20 OA 1 ADN O3' 5 -0.606 15.9994
21 H 1 ADN H06 5 0.482 1.0080
22 OA 1 ADN O5' 3 -0.246 15.9994
23 H 1 ADN H03 3 0.337 1.0080 ; -0.000
24 C 1 ADN C2 6 0.502 12.0110
25 HC 1 ADN H10 6 0.106 1.0080
26 NR 1 ADN N1 6 -0.608 14.0067 ; 0.000
Also I've done proper equilibration in tho steps (I've used 1fs
integrator steps on both stages of equilibration)
1- I've made equilibration with posres ( 500ps) on protein backbone
atoms as well as ligand with x-ray water
2- The next step (5ns) was done without posres only with smaller
integrator steps.
What another possible sollutions could be ?
Try some diagnostics:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
If simulations of the same system without a ligand run fine, then the error is
still related to the ligand, either its topology or placement.
-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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