Hi Aishwarya,
besides distances, the only other physical quantities that enter into the
calculation of moments of inertia are the masses of the particles, so
looking only at the apparent radius at VMD is not enough to say anything
about your results.
so either your systems are indeed different
Hi,
Yes of course the ratios are similar. The shapes are similar
But when I measure the distance of the two agrregates in VMD , the length
of the aggregates and the width of the aggregates are more or less of the
same dimensions. Which means that the size of the aggregates are
comparable and
Hi,
Yes of course the ratios are similar. The shapes are similar
But when I measure the distance of the two agrregates in VMD , the length
of the aggregates and the width of the aggregates are more or less of the
same dimensions. Which means that the size of the aggregates are
comparable and
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123938.html
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
Solution to what exactly?
Both sets have a ~1:3:3 ratio, I'd guess you have two prolate spheroids?
and it indicates that yes, they have a similar shape as you stated.
Or is the concern the fact that there is ~4x difference between agg1 and
agg2 I values? That indicates that agg1 is bigger than
Hi,
I am trying to find the moment of inertia of an aggregate.
I have used the command gmx gyrate -f test.gro -s test.gro -p yes -mol
yes -o out.xvg
For two aggregates the the shape is similar but the values are
very different for Ix Iy Iz
For an aggregate 1
Ix Iy
Dear All,
I am trying to understand how the actual Rg is calculated from the Rgx, Rgy
and Rgz and how those values are related to the eigen values of the
gyration tensor?
Thanks
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On 8/18/16 10:28 PM, YanhuaOuyang wrote:
Hi, I am running a REMD of a protein, which ranged from 270 to 500K in
explicit water model with 60 replicas, and I stop to analyse the REMD data
after running for 50ns. I use the demux.pl script to get the continue the
coordinate for each replica.
Hi,
I am running a REMD of a protein, which ranged from 270 to 500K in explicit
water model with 60 replicas, and I stop to analyse the REMD data after
running for 50ns. I use the demux.pl script to get the continue the coordinate
for each replica. Then I calculate the Rg value for each
Dr. Lemkul ,
thanks a lot. This really helped me . I used cluster optionin -pbc
and this seems, put whole cluster in together. I am confused with , the
description of manual that, 'Note also that if your molecules are broken
this will not work either.'. As cluster is bigger and broken so it
On 10/20/15 1:21 PM, Parvez Mh wrote:
Dr. Lemkul ,
thanks a lot. This really helped me . I used cluster optionin -pbc
and this seems, put whole cluster in together. I am confused with , the
description of manual that, 'Note also that if your molecules are broken
this will not work
Dear All,
In my simulation, a group of molecules form a big cluster. I want to
measure radius of gyration of this cluster. I know index of molecules
those are part of the cluster. Problem is, cluster is broken due
periodicity. Is it possible in gromacs, to measure radius of gyration of
this
On 10/19/15 8:12 PM, Parvez Mh wrote:
Dear All,
In my simulation, a group of molecules form a big cluster. I want to
measure radius of gyration of this cluster. I know index of molecules
those are part of the cluster. Problem is, cluster is broken due
periodicity. Is it possible in gromacs,
On 13/07/15 10:40, Daskalakis Vangelis wrote:
Dear users,
I am employing gromacs 5.05 to simulate a water cluster (spherical shape)
forming on some salt in PBC (NVT). I want to calculate the Radius of
Gyration (Rg, through g_gyrate) throughout the simulation time. I have a
I assume you mean
Dear users,
I am employing gromacs 5.05 to simulate a water cluster (spherical shape)
forming on some salt in PBC (NVT). I want to calculate the Radius of
Gyration (Rg, through g_gyrate) throughout the simulation time. I have a
forming water (spherical) cluster, but due to PBC this spherically
Thank you Peter for your reply.
I have tried 'trjconv -pbc cluster -center' before, but despite being
so slow (for around 6000 waters),
I actually get again some spikes on the Rg due to PBC. I will give it
a try again, thank you.
On 13/07/15 12:02, Peter Kroon wrote:
* Dear users,
** I am
Depending on exactly what you want to measure, gmx clustsize might be useful
for you.
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
Dear gromacs experts,
I tried to analysis the Radius of gyration of a polymer. But I found the
result of first frame was always very different.
Then I installed different vesions of gmx with or without mpi.
And I got different results.
So I used the first tutorial on
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