Thanks Justin
>
>
> On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote:
>> Hi gmx users
>>
>> I took a natural protein fold and unfolded with simulated annealing
>> molecular dynamics (SAMD). Now I have folded and unfolded structure. I
>> want to calculate statistically entropy difference of the two
HI,
I want to simulate helical peptide in TFE-water (1:1 vol) solvent.
1. From previous searches, I got to know that tfe.itp is present in
gmx.ff folder. Can I use this itp file by including it in my top file
generated during pdb2gmx.
2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrate
Sir,
Using g_cluster I clustered snapshots in md trajectory using the
command as follows
g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o
clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr
cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl cluster
Dear Gromacs users,
Can anyone please help me how can I convert a cpt file from a new to an
older Gromacs version?
Thanks
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Ah, this is a force field issue -- urey-bradley terms are not
supported free energy calculations. However, since only restraints are
changing, this warning doesn't really need to be there.
It would be relatively simple to put in a check to allow this to work,
but it might take a week or two to get
On 7/16/13 3:43 PM, Dariush Mohammadyani wrote:
Dear All,
I have set two bilayers:
1. 400 DOPC
2. 320DOPC and 80 Cardiolipin
Second one show significant curvature during NPT equilibrium and MD run
(not in NVT eq.). Is it normal?
You could be undergoing some sort of phase transition, but in
Thanks for quick reply. I fixed the issue with kB1. Below is what I have
changed in the .mdp file. I use this to run it "mpirun -np 3 mdrun_mpi -s
prefix_.tpr -multi 3 -replex 6 -dhdl a.dhdl". But I get this error (I am
using version 4.6.1):
Fatal error:
Function type U-B not implemented in ip_pe
That's a good question. My understanding and experience is the
difference in required overlap in replica exchange and expanded
ensemble methods is not significant. There are probably some more
detailed studies out there. Expanded ensemble can be somewhat more
efficient (see a paper by Park and Pa
Hi Michael,
Thanks for the reply. Just a quick follow-up. Do you think the overlap of
energy histogram between different lambdas matter for lambda-dynamics in
general? (Maybe not in this particular case or in the case of the tutorial
you just posted.) I wonder if we need as many intermediate lambd
You need to have different pull parameters at the end states. Right
now, pull-kB1 is not defined in your code, so there is nothing to
interpolate to: it assume pull-kB1 = pull-k1.
Longer scale -- one would want to define reference distances that
change with lambda within the same simulation, but l
Hi, all-
This not a problem with W-L, but is instead something that is wrong
with a particular combination of mdp options that are not working for
expanded ensemble simulations. W-L can equilibrate to incorrect
distributions because it decreases the weights too fast (more on that
later), but that
I am trying to use Hamiltonian replica exchange as implemented in Gromacs.
The idea is to use different pulling umbrella forces and then obtain a PMF
profile. I am specifically interested in exchanging force constants between
windows.
To do a quick test, I successfully ran replica exchange in whic
Dear All,
I have set two bilayers:
1. 400 DOPC
2. 320DOPC and 80 Cardiolipin
Second one show significant curvature during NPT equilibrium and MD run
(not in NVT eq.). Is it normal?
For the first bilayer, after adding the protein to the system, here also I
can see big curvature in the membrane.
D
I have a similar question here. Can anyone tell if the Wang-Landau algorithm
in lambda space is robust in that it doesn't depend on the choice of the
convergence factor (weight-equil-wl-delta), the flatness of the histogram
(wl-ratio) and/or the frequency of trial move (nstexpanded), especially in
Hi Justin,
Thanks for suggestion...and pointing out that there is problem with
topology ...now i checked ligand file..there hydrogens were not added
correctly..so swissparam tool was not correct topology .. now i corrected
it ..it works perfectly ..
Thanks a lot
Sainitin
On Tue, Jul 16, 2013 a
I am in the process of evaluating whether Gromacs is suitable for a simulation
that I'm planning to conduct, and I was hoping that more experienced users
might provide insight into whether the following is possible: I want to exclude
a subset of molecules (i.e. all but one or two ions in the sys
Hi all,
I have 3 protein-drug complexes (same protein and different drugs) i
performed 20 ns molecular dynamics simulation..using same parameters (i
mean energy minimzation parameters) ..2 of them was successful for MD
simulation..(im using Charmm 27 Force field)
But 1 drug protein complex is fa
On 7/16/13 11:05 AM, Sainitin Donakonda wrote:
Hi all,
I have 3 protein-drug complexes (same protein and different drugs) i
performed 20 ns molecular dynamics simulation..using same parameters (i
mean energy minimzation parameters) ..2 of them was successful for MD
simulation..(im using Charm
On 7/16/13 7:41 AM, Shima Arasteh wrote:
Thanks for your reply.
But would you please tell me what is known for the pull_group line? I mean are
the atom names or resid-s or residue names or know for it?
Like everything in Gromacs, these are just group names. You can use either
default
Thanks for your reply.
But would you please tell me what is known for the pull_group line? I mean are
the atom names or resid-s or residue names or know for it?
Sincerely,
Shima
- Forwarded Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
S
On 7/16/13 5:30 AM, Shima Arasteh wrote:
Hi,
Would you please let me know how can I make an index file of COM of lipid
membrane?
I guess the position of the COM of the bilayer, but how it is possible to make
an index file of this point?
I want to include this index file as the ref_group
On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote:
Hi gmx users
I took a natural protein fold and unfolded with simulated annealing
molecular dynamics (SAMD). Now I have folded and unfolded structure. I
want to calculate statistically entropy difference of the two system.
Can we do with groma
On 7/16/13 1:02 AM, Hari Pandey wrote:
Hi Gromaxers,
Thanks for previous answers.
I have to simulate reverse micelle after solvation with isooctane.My system now
is:
ISOOCTANE(solvent)+AOT(surfactant)+coreWATER.
When I do grompp, it says moleculetype SOL is redefined and lots of another
er
Hello sir,
I require to calculate binding energy using MM-GBSA method. I searched
through the manual but i did not find any. i request you to kindly guide to
as to which manual to follow to identify binding energy.
Thanking You with Regards.
Arunima Shilpi
Ph. D Research Scholar(Cancer & Epigen
Hello,
I hope the following paper may help you
http://pubs.acs.org/doi/pdf/10.1021/j100286a020
regards
Srinivas
On Tue, Jul 16, 2013 at 9:54 AM, Dr. Vitaly Chaban wrote:
> I am afraid you will need to derive it from scratch.
>
>
> There should be some studies about perchlorate salts in li
Hi,
Would you please let me know how can I make an index file of COM of lipid
membrane?
I guess the position of the COM of the bilayer, but how it is possible to make
an index file of this point?
I want to include this index file as the ref_group in Umbrella Sampling.
Sincerely,
Shima
--
Dear Justin
I found a server :
http://biophysics.cs.vt.edu/
that protonate aminoacids according to desired pH easily.
Sincerely
Fatemeh Ramezani
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Hi gmx users
I took a natural protein fold and unfolded with simulated annealing
molecular dynamics (SAMD). Now I have folded and unfolded structure. I
want to calculate statistically entropy difference of the two system.
Can we do with gromacs???
what is the correct protocol ??
best
pooja
--
I am afraid you will need to derive it from scratch.
There should be some studies about perchlorate salts in literature. Make a
search.
Dr. Vitaly V. Chaban
On Tue, Jul 16, 2013 at 6:08 AM, Sushma Yadav wrote:
> Dear users,
>
> How do I get the force-field for ClO4- ion in the gromacs?
>
>
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