majid hasan wrote:
Yes, ideally I didn't want to, but I read somewhere on mailing list that
one shouldn't use define = -DFLEXIBLE while running dynamics. So I
thought I will use restrained water...
I'll move back to -DFLEXIBLE though, if I got a successful mdrun for
restrained water.
Constraints and restraints are separate ideas.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
If you *restrain* the water, the molecules won't move. If you *constrain*
(i.e., using rigid water and not -DFLEXIBLE, which for MD you shouldn't be
doing) you fix the geometry of a molecule while still allowing it to actually move.
-Justin
Thanks,
Majid
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Fri, April 22, 2011 10:44:45 AM
*Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote:
> I just checked and DNA position should not be restrained because I
didn't use define = -DPOSRES in .mdp file. I am going to run it for a
longer time now, and use position restraints for water
>
What purpose does restraining the water have? You'll be trying to
observe diffusion of your DNA or CNT through an immobile solvent.
-Justin
> Thank You,
> Majid.
>
> ------------------------------------------------------------------------
> *From:* Mark Abraham <[email protected]
<mailto:[email protected]>>
> *To:* Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
> *Sent:* Fri, April 22, 2011 1:51:47 AM
> *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation
>
> On 4/22/2011 6:48 PM, Mark Abraham wrote:
>> On 4/22/2011 4:54 PM, majid hasan wrote:
>>> Dear All,
>>>
>>> I am doing a MD simulation of dna, and cnt in water. I get a stable
simulation in which DNA, and CNT wiggles around there positions, but
they don't seem to be attracted towards each other. CNT starts in the
middle of the box and just moves a little, and DNA starts at top right
corner of the box and remains there throughout the simulation.
>>>
>>> movie of .trr file is here:
>>>
>> http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg
>>>
>>> My .mdp files are placed here (both .mdp files are same except for
the value of integrator):
>> http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp (used for EM)
>> http://phas.ubc.ca/%7Emajid/Project/md.mdp (used for MD)
>>>
>>>
>>>
>>> I created cnt, and dna using following commands:
>>> For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select
(Selected amber99sb, and TIP3P water model)
>>> For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected
amber99sb)
>>> For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o
cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o
cntdnasol.gro
>>> In the dna.top file, amber99sb/ions.itp, and a position restraint
file was also included along with tip3p.itp. I mentioned it because I am
not sure why would it add ions and position restraints on adding water?
>>
>> #including molecule .itp files adds nothing to the system - only the
potential to have molecule type(s). The system is defined in the
[system] directive, and must match the corresponding coordinate file.
>>
>>> It seems that something is wrong with non-bonded interactions, but
I don't understand what?
>>
>> Why aren't you following a proper equilibration protocol before
trying to make observations? You might be using position restraints,
have your species too far apart, or simply have not simulated long
enough to observe any movement. 200ps is an eye-blink.
>
> Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is
unreasonably short. 100,000 of them is far too short to see anything happen.
>
> Mark
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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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