Dear Carlos, Tom and Bruno,
>From what I understood by "playing" with my trajectory and your very
useful comments I should probably increase the size of my cell
(and this time I will hack the topology file so that to have only
one molecule as solute).
If I display the trajout imaged trajectory, at some point, I still see
one monomer
separated from the three other monomers, hence I assume that
Tom and Bruno are right: my cell is too small.
Using a cut off equal to 10 Angs I thought that a closest distance of 11 angs
would have been appropriate for the physical behaviour of my system:
solvateoct tetramer TIP3PBOX 11.0
But apparently this box is too small.
Another thing I should probably point out is that I generated the trajectories
with NAMD (using Amber coordinates and topology files), anyway I carefully
checked my settings through the following page:
http://ambermd.org/namd/namd_amber.html
And what I derived myself are the x, y and z values for NAMD
cellOrigin keyword through
these commands in VMD:
% set sel [atomselect top "all"]
% measure center $sel
i. e. I assumed that the origin of the cell is equivalent to the geometric
center of my system, am I wrong in this? Could this be the problem of
re-imaging?
Thanks a lot for your hints.
All the best,
Il 27 settembre 2011 22:39, Bruno Rodrigues <bbrodrigues.gmail.com> ha scritto:
> What happens when you load the wrapped trajectory, like in Carlos' script?
> What does really happen with the solute. It can then give a good indication
> about what is wrong. Does one or two strands go to the next cell? Or does
> the system has any kind of sharp denaturation (probably not, but we never
> know...)?
>
> I've learned some stuff from my work with RMSD, and it sounds that a part
> of your molecule really went to the next cell. And I tell you more, the
> distance between 2 cells is around 20-25 angstroms, which means that you
> have a 12 angstroms solvent layer around your solute. I would say that it's
> too few for a 44 residues molecule. I use 12 angstroms for a 20 residues.
> Maybe someone more experienced can tell something more.
>
> On Tue, Sep 27, 2011 at 6:14 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> to follow up on Tom's last sentence ("make it so all the molecules are
>> together in the prmtop"), here is a bit of info on how to do it:
>>
>> Modify the pointers in your prmtop so that all the solute molecules are in
>> 1
>> "molecule"
>>
>> - here is a sample prmtop for a dimer- the goal is to put both monomers
>> into a single "molecule"
>>
>>
>> %FLAG SOLVENT_POINTERS
>> %FORMAT(3I8)
>> 830 10924 3
>>
>>
>> -
>> - this data is really in this format
>>
>>
>> FORMAT(12I6) IPTRES, NSPM, NSPSOL
>> IPTRES : final residue that is considered part of the solute,
>> reset in sander and gibbs
>> NSPM : total number of molecules
>> NSPSOL : the first solvent "molecule"
>>
>>
>> -
>> - what you need to do is to
>> - leave IPTRES alone (your solute is not changing)
>> - change NSPM to match your "new" # molecules (if you make a dimer
>> into a single molecule, subtract 1. if you make 3 molecules
>> into 1, subtract
>> 2).
>> - change NSPSOL the same way- subtract 1 or 2 or more, depending on
>> what you subtracted from NSPM
>> - here is the "new" SOLVENT_POINTERS section that turns the 2 monomers
>> in a single molecule:
>>
>>
>> %FLAG SOLVENT_POINTERS
>> %FORMAT(3I8)
>> 830 10923 2
>>
>>
>> - now for the next section to change- atoms per molecule.
>>
>>
>> %FLAG ATOMS_PER_MOLECULE
>> %FORMAT(10I8)
>> 6015 6015 3 3 3 3 3 3 3
>> 3
>> 3 3 3 3 3 3 3 3 3
>> 3
>>
>>
>> -
>> - what you want to do is combine the first two "molecules" (the
>> monomers) into a single molecule.
>> - change the "atoms per molecule" to combine the atoms from the two
>> molecules
>> - in this case, 6015+6015=12030
>> - move the numbers up- in this case, change the second 6015 to a 3,
>> and delete the last 3 at the end of this section.
>> - here is the modified section (not showing the removal of the final 3
>> from the end of this section- bu make sure you delete it).
>>
>>
>> %FLAG ATOMS_PER_MOLECULE
>> %FORMAT(10I8)
>> 12030 3 3 3 3 3 3 3 3
>> 3
>> 3 3 3 3 3 3 3 3 3
>> 3
>>
>>
>> - *SAVE THIS TO A NEW FILE NAME, MAKING IT CLEAR BY THE NAME THAT YOU
>> MODIFIED THE MOLECULE POINTERS*
>>
>>
>> On Tue, Sep 27, 2011 at 4:55 PM, Thomas Cheatham III <tec3.utah.edu>
>> wrote:
>>
>> >
>> > > I try to resend my email that probably was not read/received.
>> > > Any hint to fix my RMSD values would be really appreciated.
>> >
>> > There is probably not an easy way to fix. Look through the archive as
>> > suggested about imaging issues and try things like center only the first
>> > residue of each chain, etc. and imaging. Imaging based on the first atom
>> > rather than center of mas, etc.
>> >
>> > This was what prompted the question on the reflector back to you about
>> box
>> > size / amount of solvent. Likely there is too little, so there is not an
>> > easy way to, by generic procedure, image the molecules back since the
>> > periodic image may be closer than the unit cell, i.e. once it is wrapped,
>> > it becomes closer to its image.
>> >
>> > I have been meaning to write a smarter imaging routine that would attempt
>> > to minimize distances, however I have not done this.
>> >
>> > There are ways to make it so all the molecules are together in the prmtop
>> > which will prevent this.
>> >
>> >
>> > --tec3
>> >
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>> >
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>
>
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
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>
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
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Received on Wed Sep 28 2011 - 04:30:02 PDT
