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#3208 - 08/19/06 08:19 PM Re: TFE parameter optimization [Re: greenhorn]
alex Offline

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Registered: 10/04/03
Posts: 780

TFE a tricky molecule. the condensed phase properties are not ideal; however, I am currently not working on them.

alex
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School of Pharmacy
University of Maryland
20 Penn Street
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#3209 - 08/20/06 08:17 PM Re: TFE parameters [Re: alex]
greenhorn Offline
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Registered: 05/11/06
Posts: 11
Loc: Freising, Munich, Moscow, Sain...
Dear Alex,

many thanks for your new ressources on your homepage !
...is it possible that it does not make sense to try to optimize a 2,2,2trifluoroethanol molecule model for the (current) additive Charmm force field in stead of waiting for the next generation of force fields that will allow for explicit representation of polarization effects (which could be expected to be quite important in 2,2,2trifluoroethanol/water mixtures as fluor atoms are extremely electrophilic)? If not: how much time would you say is necessary if I start as a beginner in parametrization
to build a more suitable TFE model for building good TFE/water boxes which can reproduce experimental properties more accurately ?

many thanks for your response in advance,
David

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#3210 - 08/21/06 02:51 PM other then TFE parameters [Re: alex]
prakash Offline
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Registered: 10/04/05
Posts: 206
It would be easier if i have informations other then TFE.

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#3211 - 08/28/06 09:20 PM Re: TFE parameters [Re: greenhorn]
alex Offline

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Registered: 10/04/03
Posts: 780

it will take a good amount of time as you will need to do a careful optimization of the LJ parameters, which is the most difficult aspect of the FF to optimize. I suggest you take the current model and do condensed phase simulations in different conditions for which experimental data is available. the absolute values for the empirical model may not be correct, but if you are getting the trends correct, that should be adequate for your needs.

alex
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School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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#3212 - 08/30/06 05:21 PM model_b_molvib_g03.inp shows error [Re: alex]
prakash Offline
Forum Member

Registered: 10/04/05
Posts: 206
In the tutorial of forcefiled parameters for new molecules, where i could run all the inp files except model_b_molvib_g03.inp and showing an error

charmm/c32b1/exec/gnu/charmm < model_b_molvib_g03.inp > model_b_molvib_g03.out
fmt: end of file
apparent state: unit 12 named fort.12
last format: (20A4)
lately reading sequential formatted external IO
Abort

how could i rectify it and how to see the optimized charges.

thank you

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#3213 - 09/04/06 05:19 PM parameter request [Re: alex]
prakash Offline
Forum Member

Registered: 10/04/05
Posts: 206
Dear all

How could i start this molecule (attchement)to create topology file with exisiting topolgy information (analogy model) i couldnt find more examples on this topic.
thanking you


Attachments
11518-lastfigurec153.jpg (424 downloads)


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#37264 - 01/10/19 10:55 PM Re: parameter request [Re: ldemaria]
Lauren Offline
Forum Member

Registered: 01/10/19
Posts: 2
Hi all,

I realise this discussion is quite old but I would just like to ask if there are any recent TFE parameters that you can recommended for use with CHARMM force fields? Specifically as a solvent.

Thanks in advance for the help.

Lauren

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#37265 - 01/10/19 11:31 PM Re: parameter request [Re: ldemaria]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
Have you checked the CGenFF topology file, top_all36_cgenff.rtf?
_________________________
Rick Venable
computational chemist


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#37291 - 01/18/19 02:12 AM Re: parameter request [Re: ldemaria]
Lauren Offline
Forum Member

Registered: 01/10/19
Posts: 2
Dear Rick,

Thank you! I didn't realise I could find it there.

Thanks a lot,

Lauren

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