VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Oct 19 2016 - 20:49:50 CDT

Not sure how you were simulating in the first place but normally Crystal
structures have some water which are basically nascent oxygen atoms ... You
convert them to some water representation (mostly tip3p) .. Are you sure if
this was done correctly?

To simulate any system irrespective of whatever it's contents are, you need
to define it in terms of "A forcefield" ... If you use NAMD you will create
a PDB and a PSF. Then using both of these files and the respective
parameters you simulate.

Having said that, to add more waters to a system already having waters
(assuming you are using the GUI) you will have to fill in some boxes
(either the length of the box after solvation or how much to solvate in
each direction). I believe vmd solvates the entire box and then deletes all
waters within a certain cutoff of your previous system. One approach is to
delete the crystal structure waters and all the solvent using some
solvation protocol. You can also retain the crystal waters assuming correct
selections are made.

For every change in the system even by one atom the pdb changes and as its
coupled with the psf the psf must change as well. Doesn't matter what that
change is. So you have to generate a new PSF for its corresponding pdb
Everytime you delete/add something.

Please tell us how you are adding new waters, what values are you putting
into the GUI? A quick way to check is to add little solvent to see if some
waters get added? Trouble shooting is a lot easier with the command line.
Once you go through this and try out new things and if they don't work come
back and I can give you a script to add some solvent running which you will
have some output and we can better trouble shoot the problem then, if it
occurs. In your next post do answer the questions I asked above.

Best,
/A

On Oct 20, 2016 12:04 PM, "Life Sciences Inc" <contact.lifesciences.inc@
gmail.com> wrote:

> Basically I had a system who I was simulating already (lipids + water ) so
> I added force field and created psf and pdb, then later on I felt to add
> more water in the already running system I stopped simulating it and then
> added more water, by seeing different tutorials I noticed that yes
> Solvation should be the next step after running autopsf (and also it takes
> long time) but I was afraid that as I have added new water molecules so I
> have to again add force field, thats why I added water molecules first and
> then run autopsf to add forcefield and to get new psf and pdb files (but
> the screen is getting held without any response, I tried with ions and
> water.str file combined with force field then autopsf is running and making
> the psf and pdb files, but also deleting many of the water molecules)
>
> for future reference:
>
> that means I don't have to add force field again whenever I am just adding
> new water molecules in the system ? I have to add force field when I add
> protein or some other molecule, is that right ?
>
> On Wed, Oct 19, 2016 at 11:33 PM, Life Sciences Inc <
> contact.lifesciences.inc_at_gmail.com> wrote:
>
>> Basically I had a system who I was simulating already (lipids + water )
>> so I added force field and created psf and pdb, then later on I felt to add
>> more water in the already running system I stopped simulating it and then
>> added more water, by seeing different tutorials I noticed that yes
>> Solvation should be the next step after running autopsf (and also it takes
>> long time) but I was afraid that as I have added new water molecules so I
>> have to again add force field, thats why I added water molecules first and
>> then run autopsf to add forcefield and to get new psf and pdb files (but
>> the screen is getting held without any response, I tried with ions and
>> water.str file combined with force field then autopsf is running and making
>> the psf and pdb files, but also deleting many of the water molecules)
>>
>> for future reference:
>>
>> that means I don't have to add force field again whenever I am just
>> adding new water molecules in the system ? I have to add force field when I
>> add protein or some other molecule, is that right ?
>>
>> On Wed, Oct 19, 2016 at 9:25 PM, Peter Freddolino <petefred_at_umich.edu>
>> wrote:
>>
>>> When you say that it is getting held, is there any output going to the
>>> console? Do you have an hourglass/spinning lollipop/busy indicator for your
>>> mouse cursor when vmd is active? How long have you waited?
>>> The ideal workflow is to run autopsf and THEN run solvate. Autopsf will
>>> take a LONG time on a solvated system because it has to run chain splitting
>>> on all of the waters…
>>>
>>> Best,
>>> Peter
>>>
>>> > On Oct 19, 2016, at 12:13 PM, Life Sciences Inc <
>>> contact.lifesciences.inc_at_gmail.com> wrote:
>>> >
>>> > HI ALL
>>> >
>>> > I am trying to create a psf file and pdb file from autopsf , I am
>>> addding the charmm 36 force field for lipid and water molecules through
>>> topology file "top_all36_lipid.rtf". First I did solvation using Solvate
>>> tool of vmd and then I am loading the pdb file from solvate tool to be used
>>> in autopsf tool.
>>> >
>>> > Autopsf is making chains and everything is normal, but when the
>>> processing comes to the last chains of TIP3 water molecules somehow the
>>> tool is getting held and showing no error. I am using VMD 1.9.2 version--f46d040f9e72420088053f422468--