VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 31 2011 - 13:16:11 CDT

On Wed, Aug 31, 2011 at 1:28 PM, hamid mosaddeghi
<hamid592004m_at_yahoo.com> wrote:
> Dear Axel
>
> I used same condition with some paper and then I have this problem.
>
> do you write HBOND tcl in VMD? Please check it for SPC/E water.

no, but that is irrelevant here. there is _nothing_ in hydrogen
bonding analysis that needs to care about the nature of a
water potential. why should it?

> PS: my systems run under Dl_poly 2.18 and after equilibrated I used History
> file for analysis.
> condition of my system:
>
> -temperature: 300K
> -Pressure: 1-3 atm
> -density: 0.998 g/cm3
> -timestep:0.001 ns
> -I used Spc/e water with constraint see help dl_poly

i repeat, that doesn't say anything. have you made
_any_ statistical analysis on the "quality" of your data?
how do did you determine equilibration?
do you have any independent parameters,
that can confirm that you are actually correctly
reproducing the simulation in the reference?
do you use the same kind of thermostat?
what about long-range electrostatics?

you cannot just say. i ran this simulation,
i use this script and it doesn't give the same
number, so the script has to be wrong.

axel.

> Best Regards
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: hamid mosaddeghi <hamid592004m_at_yahoo.com>
> Cc: vmd <vmd-l_at_ks.uiuc.edu>
> Sent: Wednesday, August 31, 2011 5:15 PM
> Subject: Re: vmd-l: Hbond in VMD
>
> On Wed, Aug 31, 2011 at 4:12 AM, hamid mosaddeghi
> <hamid592004m_at_yahoo.com> wrote:
>> Dear all
>>
>> I counted Hbond from VMD for SPC/E water model in normal condition , I got
>> 2.56 Hbond per/molcule but more paper reported 3.~ 3.3 Hbond per/molcule
>> why?
>
> there are a _ton_ of possible reasons.
>
>> I used Cutoff angle 30 and cutoff distance 3.5 A from literatures.
>
> that still doesn't mean you are using the exact same definition of
> hydrogen bonds, and more importantly, it doesn't say anything about
> whether your simulation has been properly equilibrated and is simulating
> the exact same region in phase space. did you do any statistical error
> estimates?
>
> axel.
>
>> Best regards
>>
>> Hamid Mosaddeghi
>>
>> Phd Student Of Physical Chemistry
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.