Dear Sir,
I have found in literature that most of the unfolding studies of proteins are performed at higher temperature by increasing box size accordingly. My protein has approximately 70 residues, I want to simulate it at room temperature as well as at some higher temperatures. I have not
Hi Sangeeta,
1) Will the result be erroneous if I keep box size unaltered at higher
temperature?
If your protein starts unfolding, you are likely to get direct
interactions between your periodic images. That will severely distort
your results (to the point that you can not draw
On Wednesday 30 January 2008 23:56, Mark Abraham wrote:
There's no a priori reason why a mixture of a united-atom detergent
sodium dodecyl sulfate and an all-atom peptide *couldn't* work. Neither
is there any reason to suppose they *would* work without evidence that
the SDS parameters were
Dear Mark, Chris,
Thanks for your useful suggestions.
Yes Mark define = -DFLEXIBLE is the only difference in both the cases.
Actually in my previous post I have pasted only small section of tip4p.itp
file,(sorry if it created unnecessary confusions/doubt). This time I am
pasting full
Louic Vermeer wrote:
On Wednesday 30 January 2008 23:56, Mark Abraham wrote:
There's no a priori reason why a mixture of a united-atom detergent
sodium dodecyl sulfate and an all-atom peptide *couldn't* work. Neither
is there any reason to suppose they *would* work without evidence that
the
Hi,
You were right for the bonds, I forgot that I was using constraints = all-bonds.
Could the missing term be the soft core then ? Or is it included in VdW ?
Anyway, I noticed that this problem of hidden extra term happens when I modify
something else than a hydrogen. Does it make sense ?
For
Date: Thu, 31 Jan 2008 15:29:50 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE : FEP : separating components of dgdl
Hi,
You were right for the bonds, I forgot that I was using constraints =
all-bonds.
Could the
I think, there are some best parameters :)
Ich tested them with some smaller systems and found, that sigma=0.3 and
alpha=0.25 seem to perform quite well.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical computational biophysics department
Am
Hi all,
Somebody has sent a mail which is about the address of a server in which the
temperatures for a REMD simulation is calculated. However, I can not find this
mail. Could you sent the address of the server, please?
Thank you
Ozge Engin
=
Computational
http://folding.bmc.uu.se/remd/index.php
It's in the news section of www.gromacs.org.
Carsten
OZGE ENGIN wrote:
Hi all,
Somebody has sent a mail which is about the address of a server in which the
temperatures for a REMD simulation is calculated. However, I can not find
this mail. Could
hello users
please can you tell me how to calculate surface area per lipid, orer
parameters, area per head group of lipid from simulation
thanks in advance
_
Post ads for free - to sell, rent or even buy.www.yello.in
Hi Pragya,
well:
-Surface area / lipid: = x(box)*y(box) / half the number of lipids in
your box
-order parameter: see the g_order-tool
-3rd one I can't say, but a general hint:
Search on www.gromacs.org in the mailing list archive, most of these
topic has been discussed a thousand times before.
On Thursday 31 January 2008 18:36, pragya chohan wrote:
hello users
please can you tell me how to calculate surface area per lipid, orer
parameters, area per head group of lipid from simulation thanks in advance
There are different methods to calculate the area per lipid, check the
Thanks Maik for your advice. I think what I'm going to do is to look
at the relative binding free energy differences between the bases.
Thus, I will morph the bases into one another, leaving the sugar and
phosphate intact. Do you think this is a better strategy?
Thanks,
Bob
On 1/28/08, Maik
There's no a priori reason why a mixture of a united-atom detergent
sodium dodecyl sulfate and an all-atom peptide *couldn't* work.
Neither is there any reason to suppose they *would* work without
evidence that the SDS parameters were developed with this purpose in
mind and suitably
Hi gmx-users,
I would deeply appreciate if anybody generously share his DPhPC lipid structure
for GROMACS simulation.
Thank you in advance for your kind consideration.
Jae H. Park
===
Jae Hyun Park, Ph.D.
Research Scientist
3215 Beckamn Institute
University
[EMAIL PROTECTED] wrote:
Dear Mark, Chris,
Thanks for your useful suggestions.
Yes Mark define = -DFLEXIBLE is the only difference in both the cases.
Actually in my previous post I have pasted only small section of tip4p.itp
file,(sorry if it created unnecessary confusions/doubt). This time
[EMAIL PROTECTED] wrote:
There's no a priori reason why a mixture of a united-atom detergent
sodium dodecyl sulfate and an all-atom peptide *couldn't* work.
Neither is there any reason to suppose they *would* work without
evidence that the SDS parameters were developed with this purpose in
Hello All,
I am getting some weird behavior with the pull code. Note I am running a
windows 64 port of 3.3.1. When I run the pull code and have nstxtcout set
to any value but 1 in my mdp file, I get garbage in my .pdo file as output.
The output shows my pull group as essentially frozen except
As long as you morph pyrimidine into pyrimidine and purine into purine,
everything is fine, I'd say.
Morphing a pyrimidine into a purine is really problematic, cause you
have to morph the whole nucleoside. Until now I didn't find a
possibility to do that without perturbing all atoms of the
Hi Angel,
If the transformation can not be analytical, I could fit (numerically)
the parameters of the Ryckaert-Belleman potential to the function that
results from the original one... Although this is not probably the best
way of using the force field as originally proposed, the difference
21 matches
Mail list logo
