AMBER Archive (2005)

Subject: Re: AMBER: Re: TI tutorial

From: Jiten (jiten_at_postech.ac.kr)
Date: Wed Jun 29 2005 - 12:24:19 CDT

Dear D. Case,

Thanks for your reply. I will try both ways and let you know when I finish
the calculation. I have just two more question

Considering the charge and vdW changes separately,

For the changes on vdW parameters.

1. What should be the starting geometry for this calculation : my originally
equilibrated geometry OR from final geometry of charging TI calculation ?

2. In your TI tutorial the CHARGE and DELTA.charge column are kept zero as
the
system was alreay been neutralized. However, in my case the charges of the
system is with that of GLY (as previously ALA --> GLY charge transformation
are done). Therefore, should I keep both the CHARGE and DELTA.charge column
with that of GLY and zero respectively.

I am sorry for many simple (still doubting in my mind) questions.

Sincerely,

Jiten

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, June 30, 2005 2:01 AM
Subject: Re: AMBER: Re: TI tutorial

> On Thu, Jun 30, 2005, Jiten wrote:
>>
>> Therefore, both the charge and vdW parameters changes are to be done in
>> one
>> step
>
> I don't recommend this, but you can try it to see what happens. It is
> more
> usual to change the charges and the vdW parameters in separate steps, as
> in
> the tutorial. But trying things both ways might be very instructive.
>
> ...dac
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu