VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Fri Jun 22 2018 - 09:07:03 CDT

Dear Muthukumaran

you are almost right. Solvate loads wat.top topology file that only
contains the topology of TIP3P water model. The file presents itself as a
topology of CHARMM22, but the topology of TIP3P of CHARMM36 is identical.
Again, I am talking about the topology, not the parameters. So, you can use
this topology file, and solvate plugin in its turn, to solvate your system
for CHARMM36. Just remember to use the toppar_water_ions_namd.str as
parameters input in your simulations.

I hope this helps

Best

João

On Fri, Jun 22, 2018 at 2:32 AM Muthukumaran Rajagopalan <
kumaran_at_bicpu.edu.in> wrote:

> Dear VMD users,
>
> I am solvating a bilayer using "solvate 1.7" plugin of vmd 1.9.3 version.
> The solvate plugin is reading the "topology file
> /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.7/wat.top". The wat.top
> files contains "CHARMM22 Proteins and CHARMM27 Lipids" but I need to use
> the Charmm36 for bilayer and corresponding TIP3P.
>
> When bilayer is solvated with Charmm27 TIP3P water model and simulated
> with Charmm36 force field causes the reduction in the area per lipid (APL)
> and bilayer enters gel phase was reported in literature.
>
> And also, I read the previous thread in vmd mailing "
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28230.html". As
> per the thread, it was mentioned vmd 1.9.3 version uses new C36 topology
> files but in my case it still loads the load charmm22/27 force field.
>
> Any help regarding how to use c36 waters will be very helpful..
>
>
>
> R. Muthukumaran
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851