On 12/8/13 2:38 PM, bahareh khanoom wrote:
Dear friend
very thanks for your answers

There is one important thing that i must say, after minimization energy i
run my system for nvt equilibration in " 500 ps " and run done without any
problem ,
then i applied the output file as input file for nvt equilibration in "15
ns" , but during first "1 ns" run exit:

Step 79777, time 159.554 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.346309, max 1.958716 (between atoms 13 and 15)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      13     15   90.0    0.1000   0.2959      0.1000
Wrote pdb files with previous and current coordinates

so ,what is your suggestion for solving this problem?


The same as I suggested in my previous message. You need to (scientifically!) diagnose the possible sources of error.

-Justin

thanks in advance
bahar


On Sat, Dec 7, 2013 at 4:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 12/7/13 4:51 AM, bahareh khanoom wrote:

Dear friend
thanks for your answer

first i generate" DRG.itp" for adsorbed molecules, by PRODRG server.
next i optimize adsorbed moleculs by gaussian
b3lyp/6-311++g(d) opt Pop=ChelpG
and the end ,i replaced the charges in" DRG.itp" with  charges that
produced by gaussian.


How do these charges compare with existing charges for similar functional
groups in the force field?  AFAIK, there is no hard evidence as to which QM
method will give the best results from Gromos96 force fields.


  so ,what is the reason?


It is hard to say at this point, but one solution is to simulate each
component individually to verify that their topologies are correct and that
your .mdp settings are appropriate (though they look reasonable on first
glance).

See also http://www.gromacs.org/Documentation/Terminology/
Blowing_Up#Diagnosing_an_Unstable_System.


-Justin

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Justin A. Lemkul, Ph.D.
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School of Pharmacy
Health Sciences Facility II, Room 601
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==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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