[gmx-users] Implicit solvent MD is not fast and not accurate.

[xiao]

Dear Justin,
Thank you very much for your suggetions.
BW
Fugui


At 2013-03-27 22:15:23,"Justin Lemkul" <jalemkul at vt.edu> wrote:
>On Wed, Mar 27, 2013 at 10:11 AM, xiao <helitrope at 126.com> wrote:
>
>> Dear Justin,
>> Thank you very much for your reply.
>> I found that the speed of implict MD is slower that explict MD. For
>> examplex, the speed of an explict MD for a protein of 300 amino acids is
>> about 3ns per day, however, the implicit solvent is about 1.5ns per day.
>>
>
>I know. This is what I mean about the need for improving the capabilities
>of the code. The main point of the implicit solvent approach is that it
>should be faster.
>
>
>> With respect to the accuracy of implicit solvent, the result shows bad
>> result. There are two carbon atom types which are not in the gbsa.itp, and
>> i just copied some carbon atom type in gbsa.itp because i find that there
>> is no big difference between the carbon parameters. I do not know whether
>> this is the
>
>reason.
>>
>
>You need to establish whether what you did was appropriate or not before
>you begin accusing Gromacs of being inaccurate.  If you observe
>inconsistencies, errors, poor energy conservation, etc. in the context of
>some known system, then that might be worth investigating.  Problems with a
>custom topology are more likely to be due to the topology than to the
>software using it.  GB atom types are one possible source of error, but in
>parametrization, there are plenty of things that can go wrong before you
>even get to that point.
>
>-Justin
>
>-- 
>
>========================================
>
>Justin A. Lemkul, Ph.D.
>Research Scientist
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540)
>231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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