From owner-nwchem-users Tue Jan 28 09:23:03 2003 Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.8.8+Sun/8.8.5) id JAA28100 for nwchem-users-outgoing; Tue, 28 Jan 2003 09:03:31 -0800 (PST) Date: Tue, 28 Jan 2003 17:58:52 +0100 From: Volkhard Helms Subject: Re: Modification of solute molecule To: Jayjr , nwchem-users@emsl.pnl.gov Message-id: <3E36B6CC.1010001@mpibp-frankfurt.mpg.de> MIME-version: 1.0 Content-type: multipart/alternative; boundary="------------050703010908010606060200" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-DE; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: de-DE References: <20030128163421.84477.qmail@web40802.mail.yahoo.com> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk --------------050703010908010606060200 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, yes, you can compute with NWChem the free energy difference between two systems that are specified by different parameter sets. Each atom is described by three parameter sets and you can perform a free energy perturbation calculation between two sets. An example of how to run a MCTI (multi-configuration thermodynamic integration) calculation is the example file crown.nw in ../nwchem/examples/md/crown As a default, the prepare task will give the same parameters to sets 1 - 3 of, say, methanol. Using the prepare directive "modify atom set 2" you can change the entries of set 2 to those of methane and then perform a MCTI calculation. I don't have a good example file at hand, unfortunately. With best regards, Volkhard Helms Jayjr wrote: > Hi. > Would it be possible to modify a solute molecule > within a solution? For example, a methanol molecule > surrounded by water molecules, would it be possible to > modify methanol into methane using the prepare module? > If so how? Thank you. > > > ------------------------------------------------------------------------ > Do you Yahoo!? > Yahoo! Mail Plus > - > Powerful. Affordable. Sign up now > --------------050703010908010606060200 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,

yes, you can compute with NWChem the free energy difference between
two systems that are specified by different parameter sets.
Each atom is described by three parameter sets and you can perform a
free energy perturbation calculation between two sets.

An example of how to run a MCTI (multi-configuration thermodynamic
integration) calculation is the example file crown.nw in
../nwchem/examples/md/crown

As a default, the prepare task will give the same parameters to sets 1 - 3
of, say, methanol. Using the prepare directive "modify atom set 2" you can
change the entries of set 2 to those of methane and then perform a MCTI
calculation.

I don't have a good example file at hand, unfortunately.

With best regards,
Volkhard Helms

Jayjr wrote:

Hi.
Would it be possible to modify a solute molecule
within a solution? For example, a methanol molecule
surrounded by water molecules, would it be possible to
modify methanol into methane using the prepare module?
If so how? Thank you.

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Yahoo! Mail Plus - Powerful. Affordable. Sign up now

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