Dear all,
I have performed REMD for a system containing Protein, Reline, Urea and
Water in the temperature range 290 to 450 K consist of 16 replicas out of
47 replicas generated by REMD temperature generator. But after the MD
simulation the exchange probability is zero. I have used position
res
Dear Justin,
Thanks for your answer.
I rechecked box dimension (along Z) and corrected it. My problem was
solved.
Best,
Atila
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Hi all,
Excuse me for my questions.
After energy minimization, I did NVT equilibration phase. Unfortunately, I
did not find an appropriate tutorial and mdp file for CNT simulation. I
used following mdp file:
integrator = md
nsteps = 5
dt = 0.002
energygrps = CNT LIG
nstxout = 500
nstvou
How frequently are you trying to exchange?
===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillis
On 7/19/18 11:54 PM, Joshua Cummings wrote:
Hi Everyone,
I'm currently trying to run some simulations that involve the absorption of N2
into a liquid solvent. I'm having some difficulty in generating the topology
for N2. For reference, the pdb file I have for N2 is as follows:
HETATM
On 7/20/18 2:42 AM, Apramita Chand wrote:
Dear All,
In my previous posts, I had written about errors arising upon changing the
combination rule and using sigma and epsilon values. Dr Lemkul was kind
enough to point out that incorrect formatting of the ffnonbonded.itp might
cause errors and tha
I have tried an exchange every 2 ps. That is every 1000 steps.
On Fri, Jul 20, 2018 at 5:34 PM, Smith, Micholas D.
wrote:
> How frequently are you trying to exchange?
>
> ===
> Micholas Dean Smith, PhD. MRSC
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge N
Hello,
The REMD generator provides an estimate of the number of replicas that may
be necessary (based on the system size) for performing replica exchange
properly. Since you got 47 replicas, you can maybe play around with
replicas more or less around that range. Maybe 16 replicas is much less for
Dear Mark,
Sorry for late reply of your queries. Frankly speaking I am planning to run
a REMD for 50ns with protein urea and water in it, then after 50ns I want
to add a protecting osmolyte into the system and want to continue it for
another 50ns REMD so that I can have the effect of the protecting
Dear Krieger,
Frankly speaking I am planning to run a REMD for 50ns with protein urea and
water in it, then after 50ns I want to add a protecting osmolyte into the
system and want to continue it for another 50ns REMD so that I can have the
effect of the protecting osmolyte before and after adding i
Hi,
You can't arbitrarily choose both the temperature range and number of
replicas and get non-zero exchange probability. See
https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r. For a
given average exchange probability, choose a range and thus the number of
replicas, or the number
Hi,
You haven't answered the question clearly. Do you care about observing the
transition (whose properties will depend on how you introduce the mixing),
or just the difference between before and after? Your proposed method is
ill formed because you can't continue a simulation after fundamentally
I want to see the helix transition.. whether it is coming back or not in
the presence of the protecting osmolyte where urea is already there in the
system
On Sat, 21 Jul 2018, 2:21 am Mark Abraham, wrote:
> Hi,
>
> You haven't answered the question clearly. Do you care about observing the
> tran
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