Re: how to use ethanol as solvent in namd for MD simulations?

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Fri Jul 31 2009 - 07:59:03 CDT

Hi Jian,

I haven't such problems with Vega so far, meter of fact all calculation
prepared by Vega run on NAMD 2.6 or 2.7 without problem until
completition. Maybe you have problem with parameter sets available,
direction to which should be specified in NAMD inputs. It will be useful
to offer address were data given on
http://www.mdbbs.org/thread-13166-1-1.html could be found in English.

Sincerely

Branko

Jian Liu wrote:
> Hi all,
> I think VMD can deal with it perfectly,
> and the full way is discussed in
> http://www.mdbbs.org/thread-16499-1-1.html (Chinese).
>
> VegaZZ is not compatible with VMD/NAMD well,
> there is a bug (maybe) in VegaZZ's psf/pdb file in
> http://www.mdbbs.org/thread-13166-1-1.html (Chinese),
> I am not sure weather VegaZZ can generate the psf/pdb file with
> proper atom name and atom type which are readable by NAMD
>
> sincerely
> Jian Liu
>
>
>
> ----- Original Message -----
> From: Branko <bdrakuli_at_chem.bg.ac.yu>
> To: Wang Yf <yunfenwang126_at_126.com>, namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: how to use ethanol as solvent in namd for MD
> simulations?
> Date: 2009-7-31 17:50:17
>
> Hi Wang,
>
> Try to use VegaZZ (free software @
> http://www.ddl.unimi.it/vega/download.htm) to build cluster and
> prepare your input. Vega can be used as NAMD (2.6 and 2.7b1) GUI and
> offer user-friendly solvent cluster builder, as well as solvation tool.
>
> Branko
>
> Wang Yf wrote:
>>
>> dear all,
>> how to use ethanol as solvent in namd for MD simulations ? could
>> anyone can describe it in detail for me ?
>> thanks a lot in advance!
>> sincerely,
>> wang.
>>
>>
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