[gmx-users] UV radiation (David van der Spoel)

Groenhof, Gerrit ggroenh at gwdg.de
Thu Feb 23 08:58:49 CET 2017


On 22/02/17 13:15, Sameer Edirisinghe wrote:
> Dear Users,
> I need to simulate my polymer system under UV radiation ( or photons) as i
> want to study the UV behavior of the polymer system. Can anyone please
> suggest me a method to do that with gromacs.
> Regards
> Bhagya Karunarathna
> That is basically an electric field that can be modelled in gromacs,
> check this paper: http://dx.doi.org/10.1002/anie.200703987

UV frequency is a bit higher than any vibrational frequency and couples to electrons.

What method to use will depend on what you want to investigate. If you're interested in the consequences of UV absorption on a small part of the polymer, you can use QM/MM, with a QM method suited for excited state, such as CASSCF, CIS, or TDDFT in combination with surface hopping. This has been done with gromacs, see for example: http://pubs.rsc.org/en/content/articlelanding/2012/cp/c2cp23628a#!divAbstract

Alternatively, if you understand the process, you can perhaps create an effective forcefield for the excited state, but this will be a very complicated task.

> However the damaging effects of UV radiation are probably not easy to
> model with classical simulations and you may be better off with some
> kind of DFT.


David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se


Message: 6
Date: Wed, 22 Feb 2017 19:51:38 -0700
From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
        Discussion list for GROMACS users
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Order Parameter for HII phase
        <CAERzrhvqAm9zEOe79GgYBa6dq1bNP0=RzmidHwe-ijvPvS4Sdw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear Gromacs users,

Unfortunately, I did not get any reply on this post.

I was wondering if anyone is aware of the original paper on g_order so that
I can understand the underlying algorithm of the options?
I am not sure how to use it for HII phase order parameters.

I found this article but I am not sure if these are the ones, as they do
not describe g_order.

"A new order parameter for tetrahedral configurations" by Chau and Hardwick
"Acyl chain order parameter profiles in phospholipid bilayers: computation
from molecular dynamics simulations and comparison with 2 H NMR experiments"
by Vermeer et al. (2007)

Thanks in advance for your comments

On Sun, Feb 19, 2017 at 10:18 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi Everyone,
> I was wondering if someone has any suggestion on the following post,
> please?
> Cheers
> Mohsen
> ---------- Forwarded message ----------
> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
> Date: Thu, Feb 16, 2017 at 3:13 PM
> Subject: Order Parameter for HII phase
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Dear Gromacs users,
> I am interested in calculation of order parameter of lipids in a HII phase.
> I am not sure about the correct command to use. Which one of the following
> should I use to be able to compare my data with deutirated NMR experiments?
> 1) gmx order  -f  md.xtc  -n  index.ndx  -s  md.tpr  -o  order.xvg  -od
> deuter.xvg  -d z  -szonly
> or
> 2) gmx order  -f  md.xtc  -n  index.ndx  -s  md.tpr  -o  order.xvg  -od
> deuter.xvg  -d z
> (In this case, there are four columns of data (x, y, z for each carbon
> atom).
> The column 3 seems to be the same with when we include -szonly)
> or anything else?
> Corresponding available experimental data, I assume the second command
> should be correct in my case . However, I am not sure x or y or what to use
> for judging.
> Cylinders in HII phase are parallel to the Z axis in my system.
> Many thanks in advance for your comments
> Mohsen
> --
> *Rewards work better than punishment ...*
> --
> *Rewards work better than punishment ...*

*Rewards work better than punishment ...*


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