Hi Guys,
I am trying to calculate the excluded volume of some crowders.
But the result volume is larger than the entire system box volume.
May somebody could tell me what's wrong with my calculation?
The module I used is g_sas with an additional option "-tv".
Thanks a lot.
.
Regards,
Yin Jian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel
Sent: Tuesday, January 01, 2008 8:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] problem of pr.mdp file
sudheer wrote:
>
> hi gmx users
>
stand me a little better?
Regards
Yin Jian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham
Sent: Wednesday, December 26, 2007 8:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Brownian dynamics
Yin Jian wrote:
> Hi M
stand me a little better?
Regards
Yin Jian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham
Sent: Wednesday, December 26, 2007 8:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Brownian dynamics
Yin Jian wrote:
> Hi Mark,
year
Regards,
Yin Jian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham
Sent: Monday, December 24, 2007 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Brownian dynamics
Yin Jian wrote:
> Hi Berk,
> I am looki
GROMACS users
Subject: Re: [gmx-users] Brownian dynamics
Yin Jian wrote:
> Hi Berk,
> I am looking for a way to be able to run MD faster without
> Explicit solvent component. Brownian dynamics (I mean langevin
> Dynamics) is way out I think. But I am not sure the package
> Implemented
, right?
Happy new year and merry Xmas
Regards,
Yin Jian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess
Sent: Thursday, December 20, 2007 10:21 PM
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] position restraints with npt ensemble
It will
Hi Zhenhai,
anyway the bonded(bond lengths, bond angles, and dihedral angles) and
nonbond energies can be calculated by hand with the geometry information
stored in pdb (xtc/trr) and the force field parameters.
Regards,
Jian Yin
Research Staff
E5-04-19
Singapore-MIT Alliance (SMA)
National Uni
Spoel
Sent: Friday, October 12, 2007 1:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results
Yin Jian wrote:
>
> Hi Mark,
> Since I have only a user account, I cannot install the version 3.3.2
> by myself into our system.
] On Behalf Of Mark Abraham
Sent: Friday, October 12, 2007 10:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results
Yin Jian wrote:
> Hi David,
> I used g_sas modules in version 3.3.1 and 3.3.2 but got not the Same
> results a
.
Regards,
Jian Yin
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham
Sent: Friday, October 12, 2007 10:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results
Yin Jian wrote:
> Hi David,
Hi David,
I used g_sas modules in version 3.3.1 and 3.3.2 but got not the
Same results as follows
tail sas331.xvg sas332.xvg
==> sas331.xvg <==
399982 20.4122 3.54058 23.9528 25.8919
399984 20.3506 3.38663 23.7372 27.7211
: Re: [gmx-users] 3.3.2 volume
Yin Jian wrote:
> Thanks, Christian.
> Sorry for my typo of missing the word "g_sas" before the
> Module.
> Anyway, I got surface area about 25, but volume about 3.5.
> Is that rational?
Yup... see http://en.wikipedia.org/wiki/Koch_snowflak
style. See the xmgrace manual.
Yin Jian schrieb:
>
> Hi David,
> I have used the module in 3.3.2 version to calculate the volume
> time series. I wonder what is the legend "Volume (nm\S3\N)" in
> the output file.
>
> Regards,
> Jian Yin (PhD)
> __
Hi David,
I have used the module in 3.3.2 version to calculate the volume
time series. I wonder what is the legend "Volume (nm\S3\N)" in
the output file.
Regards,
Jian Yin (PhD)
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org
Hi Erik,
What criteria gromacs uses in g_dih calculation? I mean what is the
dihedral transition
defined in this module. Thanks in adv.
Regards,
JY
___
gmx-users mailing listgmx-users@gromacs.org
http
Hi All,
Can anybody tell me more than that in the gromacs manual, how Gromacs
calculate g_sas. What are their criteria basis on hydrophobic and
hydrophilic?
Thanks in adv.
Regards,
Jian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess
Sent: Mo
r centers.
Cheers,
Erik
On Jul 20, 2007, at 11:05 AM, Yin Jian wrote:
> Thanks a lot, Hess.
> By the way, what is the cutoff criteria used in Gromacs, is it
> nonzero overlap between LJ-spheres or the mass-centers reside
> in the LJ-sphere? Since these two are significantly different
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess
Sent: Friday, July 20, 2007 4:56 PM
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] FW: rvdw
>From: "Yin Jian" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS u
Hess
Sent: Friday, July 20, 2007 4:30 PM
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] FW: rvdw
>From: "Yin Jian" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: "Discussion list for GROMACS users"
>Subject: RE: [gmx-users] FW:
x-users] FW: rvdw
>Date: Fri, 20 Jul 2007 09:11:35 +0200
>
>
>
>
>>From: "Yin Jian" <[EMAIL PROTECTED]>
>>To: "Berk Hess" <[EMAIL PROTECTED]>
>>Subject: rvdw
>>Date: Thu, 19 Jul 2007 12:53:00 +0800
>>
>>Hi Dr Berk H
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