Re: using TIP4P 2005 in namd

From: V.Ovchinnikov (ovchinnv_at_mit.edu)
Date: Wed Feb 23 2011 - 15:54:26 CST

Ana,

1)

I believe ECHH and ECHA are atomic electronegativity and hardness
parameters used in the Charge Equilibration Method (CHEQ) to model
polarization. Basic information on the method and references can be
found in the CHARMM documentation :

http://www.charmm.org/html/documentation/c35b1/cheq.html

I do not know the status of CHEQ implementation in NAMD.

2) http://www.charmm.org/html/documentation/c35b1/rtop.html (entry G11);
the line you quote states that, if a water molecule is placed at the
beginning or the end of a segment, no patches are to be applied to this
molecule.

Regards,
Victor

On Wed, 2011-02-23 at 18:57 +0100, Ana Celia Vila Verde wrote:
> Hi,
>
> I want to simulate TIP4P2005 water using NAMD. I had a look at the
> available threads in the namd mailing list and followed the suggestions
> given there: modify the topology file top_all30_* (which contains the
> parameters for tip4p) to use the parameters for tip4p2005 according to
> the topology tutorial given in the namd website.
>
> The tutorial explains almost everything we need to know about the
> topology file, except for the two things below:
>
> 1) the atom entries for tip4p are:
> ATOM OH2 OT 0.000 ECHH 0.00000 ECHA 0.00000
> ATOM OM LP -0.888 ECHH 68.49000 ECHA 371.60000
> ATOM H1 HT 0.444 ECHH 0.00000 ECHA 353.00000
> ATOM H2 HT 0.444 ECHH 0.00000 ECHA 353.00000
>
> What is the meaning of the fields after the charge? How does NAMD use
> them in the simulation?
>
> 2) The last line for the tip4p residue is
> PATC FIRS NONE LAST NONE
>
> What is the meaning of this line?
>
> I've searched for information on this (just googling, checking the
> CHARMM website, checking the NAMD website, checking the VMD website...)
> and could find none, so I'd be very grateful if anyone could shed some
> light on the matter.
>
> Thanks,
>
> Ana
>

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