[email protected] wrote:
Dear Justine,
No, I have 20 surfactants in my system in a pure solvent and try to see
the aggregation and adsorption properties of these molecules. I have run
them for 20ns. And now start to analyze my data.
Just in short I want to correct for periodicity! so that to get the
accurate result for my g_dist and g_rdf.
trjconv on the xxx.xtc.... Like
trjconv -f x_input.xtc -o x_out.xtc -b 19000 -e 20000 -s x_input.tpr
-pbc nojump
or I have to cluster it first.
I'm sorry to say I have no definitive answer, but you should be able to
determine this for yourself by watching the trajectory. If a cluster forms,
then clustering may be useful. If you try to use -pbc cluster, but not all of
your molecules are actually aggregating, then trjconv may loop infinitely.
Start with -pbc nojump, and perhaps iterations of -pbc mol and others, until you
obtain a trajectory you can visualize and easily assess. For the purposes of
g_dist and g_rdf, PBC should be handled intrinsically. There are other tools
(like g_rms) for which PBC will make a difference, but not likely these two.
-Justin
Rob
Quoting "Justin A. Lemkul" <[email protected]>:
>
>
> [email protected] wrote:
>> Dear Justine,
>>
>> I just checked at the archive list and found out lots of information
>> on how to correct for PBC! And if I understood it correctly is this
>> the right way to follow...
>> "If you are trying to correct for periodicity for all species in the
system
>> (protein and water) then a few iterations of trjconv may be
necessary, i.e.
>> -center (on protein), followed by -pbc nojump or -pbc mol -ur
>> compact. Using
>> trjconv is a bit hit-or-miss, and just requires a bit of playing to
>> get things working how you want them."
>>
>> trjconv -f xxx.xtc -o x_cluster.gro -b 19000 -e 20000 -pbc cluster
>>
>> grompp -f xx.mdp -c x_cluster.gro -o x_cluster.tpr
>>
>> trjconv -f xxx.xtc -o x_cluster.xtc -b 19000 -e 20000 -s
>> xx_cluster.tpr -pbc nojump
>>
>> Then I have to do anaysis on the new .tpr and .xtc...... is that
correct....
>>
>> Is this the right way to correct for periodicity... I took the idea
>> from you and Chris. I have done the RDF and distance measurement but
>> looks a bit off my RDF did not converge to 1. They recommend me to
>> do PBC correction on my system which is run for 20ns. I am doing the
>> analysis on the last 1ns (from 19-20 ns)
>>
>
> Without context, I have no idea if what you've done is right. The
> clustering algorithm is only really useful for the formation of
> clustered molecules (i.e. micelles), so if you're trying to apply it
> to something else, I don't know that it will work.
>
> -Justin
>
>> You suggestion is always helpful!
>>
>> Rob
>>
>>
>>
>>
>>
>>
>>
>> Quoting "Justin A. Lemkul" <[email protected]>:
>>
>>>
>>>
>>> [email protected] wrote:
>>>> Dear Gromacs,
>>>>
>>>> I want to correct the periodic boundry condition before analyzing
>>>> my data, how do I perform that?
>>>>
>>>
>>> Please see trjconv -h, as well as any of the thousands of posts in
>>> the list archive related to this topic.
>>>
>>> -Justin
>>>
>>>> any suggest!
>>>>
>>>> Rob
>>>
>>> --
>>> ========================================
>>>
>>> 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
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list [email protected]
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to [email protected].
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to [email protected].
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
