: Re: [gmx-users] BUG in angular removal part??
To: Discussion list for GROMACS users
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On 2011-04-26 19.38, Xiaohu Li wrote:
Hi, gromacs developers,
It seems that there is a bug regardi
Hi, gromacs developers,
It seems that there is a bug regarding the angular moment removal.
This may not be very important for many users since most of them are
doing PBC where it is irrelevant, but if you are doing cluster or if you
really care the angular momentum like I
do(I want the ang
ve at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 83, Issue 153
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=
Xiaohu Li
Post-doctoral Research Associate
gmx-users-requ...@gromacs.org wrote:
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ication where one would not be using pbc at the
> time. However, your clusters prove me wrong.
>
> In any case, as a work-around, you may want to use a bigger box, with long
> enough cut-offs, no PME.
>
> Hope this gets you started,
>
> Gerrit
>
> On 27 Jan 2011, at 21:
e access to the
> other QM-programs and cannot test this, so if you have, could you please run
> the same job with a different QM-program.
>
> Hope that helps
>
> Christoph
>
>
>
>
> On 01/26/2011 06:48 AM, Xiaohu Li wrote:
>
> Hi, All,
> I'm tr
Hi, All,
Just want to share information on this thread.
Regarding to the segmentation fault. I have found out that gromacs call
orca by write command to a buffer called buf. So for example, if the orca
path is
/usr/local/bin/orca
and the BASENAME(prefix of the *.tpr file) is longlonglongl
Message: 4
> Date: Wed, 26 Jan 2011 12:53:17 -0500
> From: Justin Kat
> Subject: Re: [gmx-users] mdrun_mpi executable not found
> To: "jalem...@vt.edu" ,Discussion list for
> GROMACS
>users
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you, I h
Hi, All,
I'm trying to see if anybody has experience of using the interface of
gromacs and ORCA(since it's free). I know that the following link gave
information on how
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
But.But, the gromacs in the above link is quite old(3.2). I
download
On Wed, Jan 19, 2011 at 4:40 PM, Xiaohu Li wrote:
>
> Message: 2
>> Date: Wed, 19 Jan 2011 23:23:12 +0100
>> From: Berk Hess
>> Subject: RE: [gmx-users] RE: Important: Bugs in NEMD calculation
>> To: Discussion list for GROMACS users
>> Message-ID:
>&
] Important: Bugs in NEMD calculation
>
> To: Discussion list for GROMACS users
>
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>
>
>
>
>
>
> > Date: Wed, 19 Jan 2011 19:13:12 +0100
>
> > From: sp...@xray.bmc.uu.se
>
: Wed, 19 Jan 2011 19:13:12 +0100
> > From: sp...@xray.bmc.uu.se
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation
> >
> > On 2011-01-19 18.36, Xiaohu Li wrote:
> > > Hi, All,
> > > I've found a bug in the
Hi, All,
I've found a bug in the NEMD calculation for viscosity. This has been
reviewed in *Hess's paper at JCP 116 209 2002.*
The version of gromacs I'm using is the development version. Notice
that this version correct a previous but of 4.5.3, where you uses NEMD, both
the term V(eq. 21
ul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
&g
Hi,
I'm trying to calculate viscosities of a few ionic liquid and has roughly
read about Hess's paper JCP 116 209, 2002.
Follows are the questions that I have
(1) For the method which uses the fluctuations of the pressure tensor using
Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis o
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