Sorry. Yes. I meant different replicas have different average pressures.
Thanks for the suggestions.
On Sun, Aug 25, 2013 at 9:06 PM, Michael Shirts wrote:
> Can you clarify - Do you mean that different replicas have different
> average pressures?
>
> WITHIN each replica, the +/- 2000 bar chang
Can you clarify - Do you mean that different replicas have different
average pressures?
WITHIN each replica, the +/- 2000 bar changing from step to step is
very common for using an atomic virial like gromacs does.
The AVERAGES of EACH replica should each be the average pressure they
are set as (+
Thanks everyone for your suggestions. Pressures for some of my replicas
fluctuate between -2000 bars to +2000 bars. I do not think that can be
termed as about right isn't it? The averages I am talking are over 1ns.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/NPT-REMD-tp5
That worked! Thanks a ton!
From: Justin Lemkul
To: Nimmy McNimmerson ; Discussion list for GROMACS users
Sent: Sunday, August 25, 2013 2:54 PM
Subject: Re: [gmx-users] 'Command not found' after installation
On 8/25/13 5:31 PM, Nimmy McNimmerson wrote:
>
Getting maximum compute performance with free tools sometimes costs
more than the advertised price ;-) Since neither Apple nor Intel are
making much money out of users like you, then you might be stuck until
clang has OpenMP support, or someone updates binutils for Mac.
Mark
On Sun, Aug 25, 2013
> Date: Sun, 25 Aug 2013 14:31:51 -0700 (PDT)
> From: Nimmy McNimmerson
> Subject: Re: [gmx-users] 'Command not found' after installation
> To: Discussion list for GROMACS users
> Message-ID:
> <1377466311.57911.yahoomail...@web122305.mail.ne1.yahoo.com>
> Content-Type: text/plain; charse
On 8/25/13 5:31 PM, Nimmy McNimmerson wrote:
Hmm... To be honest I'm a novice at installing complex things, I'm a computer
scientist by trade but I'm not very good at troubleshooting this kind of thing.
Has anyone actually installed GROMACS on mac and what did you do? (Using the
default gcc/
Pressure should fluctuate significantly. The estimator for the
pressure that is generally used is very noisy. The question is, do the
pressure averages over, say, 500 ps or 1 ns look about right?
On Sun, Aug 25, 2013 at 5:07 PM, Mark Abraham wrote:
> On Sun, Aug 25, 2013 at 6:22 PM, rahul seth
>
Hmm... To be honest I'm a novice at installing complex things, I'm a computer
scientist by trade but I'm not very good at troubleshooting this kind of thing.
Has anyone actually installed GROMACS on mac and what did you do? (Using the
default gcc/g++ doesn't work for the AVX stuff)
___
You are violating some assumption genion makes, but without any kind
of detail in the description of what you are doing, how can anyone
help?
Mark
On Sun, Aug 25, 2013 at 8:48 PM, sanjay choubey wrote:
> Hi,
> I am running a membrane protein dynamics. After adding ions i am receiving a
> fatal
On Sun, Aug 25, 2013 at 6:22 PM, rahul seth
wrote:
> Hi All,
>
> I have been trying to perform NPT-REMD with a Protein Substrate and water.
> I am trying to use md+nose-hoover thermostat and parrinello-rahman
> barostat. However, I am not quite sure about the tau-t and the tau-p that I
> should be
Hi,
I am running a membrane protein dynamics. After adding ions i am receiving a
fatal error like
Your solvent group size () is not a multiple of 15.
Kindly help me in fixing the error.
Sanjay kumar choube
Hi All,
I have been trying to perform NPT-REMD with a Protein Substrate and water.
I am trying to use md+nose-hoover thermostat and parrinello-rahman
barostat. However, I am not quite sure about the tau-t and the tau-p that I
should be using here. I paste a part of my mdp file below:
define
Thanks so much Justin,
I really appreciate your guidance and your input in this forum.
Thanks.
On Sun, Aug 25, 2013 at 6:00 PM, Justin Lemkul wrote:
>
>
> On 8/25/13 11:35 AM, MUSYOKA THOMMAS wrote:
>
>> Hello,
>> I am trying to minimize my ligand-protein structures but when I run the
>> code,
On 8/25/13 11:35 AM, MUSYOKA THOMMAS wrote:
Hello,
I am trying to minimize my ligand-protein structures but when I run the
code,
mdrun -v deffnm em.tpr
i am getting the error:
Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/gmxfio.c, line: 519
Can not o
Hello,
I am trying to minimize my ligand-protein structures but when I run the
code,
mdrun -v deffnm em.tpr
i am getting the error:
Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/gmxfio.c, line: 519
Can not open file:
topol.tpr
For more information and tips
On 8/25/13 12:01 AM, Rajat Desikan wrote:
Hi Justin,
In a recent post
(http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944)
you commented that:
"Unless you can demonstrate that your changes in cutoffs do not produce
artifacts or
On 8/24/13 11:11 PM, Gianluca Interlandi wrote:
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2
I'm confused about the difference between rlist and rlistlong. I am planning to
also setup an implicit solvent simulation with GBSA and CHARMM-FF. Would thi
Hi,
I don't have any experience with icc on Mac, but I would try either
* re-reading the icc docs to see whether you should be source-ing some
configuration file to set up the dynamic loading at run time (as well
as at compile time), and/or
* making a static build (cmake -DBUILD_SHARED_LIBS=off; b
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