VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu May 25 2017 - 22:10:03 CDT

Hi Karteek,
This should not actually be surprising, because the CG builder will just
put a bead at the center of mass of each set of four consecutively
numbered waters. If those waters are scattered all over the box, you'll
get a bead close to the middle of the box. This is the software doing
what it is supposed to do, but your input structure gives surprising
results because the input AA water has consecutively numbered residues
far from each other.

The fastest way to get a well-distributed box of CG water is instead
going to be to make a new pdb file that only has the first water out of
each group of four. CGbuilder will then make a cg bead out of each of
those waters (ignoring the missing atoms that it cannot find) and you'll
find them scattered throughout the box. Another approach would be just
to make and equilibrate a box of pure CG water, build a CG model of your
solute only, and then use the CG water as a nonstandard solvent in the
VMD solvate tool. I know I had such a water box at some point (as I
recall, this is why we wrote the nonstandard solvent interface in the
first place), but I can't seem to find it at the moment.

Best,
Peter

On 05/25/2017 06:01 PM, Karteek Kumar wrote:
> Thanks Peter for the reply.
>
> I have modified as suggested. Now, I could see 250 CG beads for the
> 1000 AA water.
> This makes sense, however, all the CG beads are mostly in the center
> of the box which does not seem right.
>
> I would expect them to be all over the space. Please find the attached
> pdb/psf files used.
>
> Thanks,
> Karteek
>
> On Sat, May 13, 2017 at 10:36 PM, Peter Freddolino <petefred_at_umich.edu
> <mailto:petefred_at_umich.edu>> wrote:
>
> Hi Karteek,
> The problem is that each of your waters is set as a different
> segment. CGBuilder won't combine atoms from different segments to
> form a bead. If you give all the waters the same segment and chain
> names, you will get the expected output.
> Best,
> Peter
>
>
>
> On 05/12/2017 05:48 PM, Karteek Kumar wrote:
>> Hi,
>>
>> Please find the attached pdb and psf files.
>>
>> Thanks,
>> Karteek
>>
>> On Fri, May 12, 2017 at 4:33 PM, Peter Freddolino
>> <petefred_at_umich.edu <mailto:petefred_at_umich.edu>> wrote:
>>
>> You would need to also send your pdb/pdf input files for us
>> to figure out what could be wrong. My guess is that your
>> waters don't have consecutive residue numbers...
>> Best,
>> Peter
>>
>>
>>
>> On 05/12/2017 11:37 AM, Karteek Kumar wrote:
>>
>> Hello users,
>>
>> I am trying to obtain the RDF for the mapped All-Atom
>> trajectory for martini CG model.
>> I have loaded 1000 AA water molecules and used
>> (Extensions -> modeling -> CG builder) to create the
>> mapped trajectory.
>> I could see 1000 beads but as Martini water CG model is
>> 4:1, I would rather expect only 250 beads.
>> Even the water.cgc shows that 4 water molecules are grouped.
>>
>> I am not understanding what I am missing? Any help on
>> this is greatly appreciated.
>> Alternatively, I would be happy to know any other methods
>> to get RDF for the mapped AA trajectory.
>>
>> Thanks in advance.
>> Karteek
>>
>>
>> water.cgc file shows
>> #########
>> CGBEGIN
>> TIP3 H2O 0
>> TIP3 OH2 0
>> TIP3 H1 0
>> TIP3 H2 0
>> TIP3 OH2 1
>> TIP3 H1 1
>> TIP3 H2 1
>> TIP3 OH2 2
>> TIP3 H1 2
>> TIP3 H2 2
>> TIP3 OH2 3
>> TIP3 H1 3
>> TIP3 H2 3
>> CGEND
>> ###########
>>
>>
>>
>
>