On 9/24/15 1:19 PM, soumadwip ghosh wrote:
Hi Mark and Justin,
actually I have simulated each item with pure SPCE water
separately for a few nanoseconds and they are absolutely fine. The
initial structure ( a small dna inside a CNT) was generated using
Packmol and may be due to this I have this error occuring each time.
Justin asked me to carefully look into the nvt.log file which I have
attached in my previous mail. But I am unable to detect any source of
The list does not accept attachments. One of us says that every day...
that error from it. Tsjerk suggested that for my system -nt has to be
kept less than 8. I tried that too but the same LINCS warning pops up.
My question is is there any way to fix the problem using some options
in the mdrun prompt? I think I have correct topologies since I am
You should upload your .log file and any pertinent .mdp file(s) and provide
links.
able to simulate each species separately. Hence, technically is there
a viable solution? Like I can tell you I deliberately kept the box
size 1000 nm3 to replicate some observations while the use of editconf
sugeested the box size should be 580 nm3 but can this be the issue? At
editconf does what it's told; I don't know how it can "suggest" anything.
Without the exact sequence of commands of what you did, this description is
really not useful.
-Justin
this point I am thinking of repeating the simulation keeping a small
box in mind. However, it would be really helpful if someone can
provide some insights in fixing this problem .
Regards,
Soumadwip
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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