Change name Cl to name CL and check name Na in forcefield you use (it could be
NA).
11 декабря 2011, 17:30 от Mark Abraham :
On 11/12/2011 11:43 PM, yp sun wrote:
The name of ion is different when using different force field You can check
which field force you use and find out h
Hi Patrick,
thanks for your help. What I still do not understand is, how I can set-up
the replica simulation starting from the two equilibrated systems. What do
I have to put into the .mdp file and in the grompp command to consider the
two equilibrated configurations and further obtain the tpr file
On 13/12/2011 11:46, gmx-users-requ...@gromacs.org wrote:
Message: 1
Date: Tue, 13 Dec 2011 17:10:01 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Force field for polymer molecule - tips
To: Discussion list for GROMACS users
Message-ID:<4ee6ec39.2090...@anu.edu.au>
Content-Type: text/plain;
Dear GROMACS users,
Total charge of my system:
Including chain 1 in system: 2041 atoms 207 residues
Including chain 2 in system: 2036 atoms 206 residues
Including chain 3 in system: 44 atoms 1 residues
Now there are 4121 atoms and 414 residues
Total mass in system 46007.483 a.m.u.
*Total ch
Hi Sundar,
Just add 0.748 Cl-
But you might want to go back through your workflow and the topology
resulting from it, to see how you ended up with a non-integer charge.
It is sort of unphysical.
Cheers,
Tsjerk
On Tue, Dec 13, 2011 at 11:59 AM, Sundargenesan wrote:
> Dear GROMACS users,
>
>
>
Dear Sir,
I finished my simulation with gromacs, but whatever orders I use to analysize
the results, I always get errors. For example, when I type:
g_density -f md.trr
It returns:
Program g_density, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr
When I type
Hi Otto,
you have to equilibrate at each lambda value! The unscaled Hamiltionian
is your lowest "temperature", say 300K, which corresponds to lambda=0.
You generate the highest "temperature" by appropriately scaling the
Hamiltonian, say 600K, which corresponds to lambda=1. Then you create n
di
Hi Yeping
El 13/12/11 13:17, yp sun escribió:
Dear Sir,
I finished my simulation with gromacs, but whatever orders I use to
analysize the results, I always get errors. For example, when I type:
g_density -f md.trr
It returns:
Program g_density, VERSION 3.3.1
Source code file: gmxfio.c, line:
Hi Patrick,
again thanks a lot for your valuable help. But I do not get my head around
how to tell grompp that for lambda=0 I would like to use the the unscaled
Hamiltonian and for lambda=1 the highest "temperature". In the tutorial the
change in temperature is a number which is passed to the pre-p
Hi Otto,
do you know how to use the free energy code in GROMACS for running
alchemical transformations (such as thermodynamic integration)? I
strongly suggest first to be confortable with that code before trying to
implement REST. In such alchemical calculations, you have to specify two
topolo
Dear Prof.
I have a doubt about my way to add antifreeze water to my system, also I think
my question looks silly but please help me for more certainty.
I changed "W" to "WF" in water.gro file of water that I downloaded from MARTINI
site and named that antifreezewater.gro , and with below comm
Dear user:
I am planning to run some simulations of a protein encapsulated using
a rigid polymer but I not sure of what approach will be better. I was
thinking in using position restraint or freeze groups. Which procedure
will not cause problems or artifacts in the simulation? Any other idea
on ho
It was a good idea to ask! You might want to try the MARTINI forum at
the cgmartini.nl web site, though.
In short the way you did it will probably fill up the box with more
water or antifreeze particle than necessary ...
As an alternative you may want to simply replace 10% of the existing
neeru sharma wrote:
Dear Gromacs users,
I am simulating a system containing a protein with covalently attached
Mg in complex with GDP.
For nvt equilibration, I have taken protein+Mg+GDP as the single group
and Water+ions as the other. The corresponding block from the .mdp file
is below:
Hi all,
Thanks for the replies!
I was originally confused due to this sentence:
"The combination of the present carbohydrate parameter set with the 53A6 force
field involves a
single change (slightly modified carbohydrate–oxygen to water–oxygen van der
Waals repulsive inter
action parameter), b
You want to keep the conversation in the list so that others may
benefit from it.
No. You need to place 1 W in the box and manually edit the gro
file to change the last 1000 into WF but most importantly in the
topology file generate two groups one with 9000 W and the other 1000 WF.
Y
Hi,
I am running MD simulation in approximately 1.25x1.25x1.25 nm box
containing 64 waters and one LiF ion pair in NpT ensemble using gromacs
4.5.5 version. I am constraining the distance between ions using pull code
and printing out force:
; COM PULLING
pull = constraint
pull
Dear Prof.
Thank you very much from your explanation.
Best Regards
Sara
From: XAvier Periole
To: Discussion list for GROMACS users
Sent: Tuesday, December 13, 2011 6:45 PM
Subject: Re: [gmx-users] antifreeze particle in martini coarse-grained
You want t
On 13/12/2011 9:59 PM, Sundargenesan wrote:
Dear GROMACS users,
Total charge of my system:
Including chain 1 in system: 2041 atoms 207 residues
Including chain 2 in system: 2036 atoms 206 residues
Including chain 3 in system: 44 atoms 1 residues
Now there are 4121 atoms and 414 residues
T
Dear Gromacs users
I have a question regarding cosine content.
I have a 50 ns trajectory and looking at the RMSD plot, i set aside the
first 5 ns as the time required for stabilization and subsequently carried
out a essential dynamics for the backbone atoms post 5ns.
But when i perform a cosin
Dear Rafael,
It really depends on the processors, GPUs, as well as whether you are
interested in performance or performance/buck. Also note, that with
GPUs you'll need considerably more atoms/core.
First of all, the E7-s are 8-core processors, so four of them is only
32 (and from what I can see i
Hi Vijayan,
cosine content should say how not-random are the movements observed in
the configuration set you have analized.
Regarding your case, this means that, even if the RMSD is stable
starting from 5ns, the protein still experiences "random" motions.
You should therefore consider as statist
Hi Mark.
>> How will pdb2gmx "know" it has to parse the monomeres.rtp file?
>It can't. You must add to an existing .rtp file.
That's a problem (and a negative surprise), because I can't just add a
new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and
CGenFF are two different things
Jernej Zidar wrote:
Hi Mark.
How will pdb2gmx "know" it has to parse the monomeres.rtp file?
It can't. You must add to an existing .rtp file.
That's a problem (and a negative surprise), because I can't just add a
new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and
CGenFF a
Thanks Justin.
I tried the simulation with Protein_GDP and Water_ions, considering that
"Water_and_ions" group will include MG. But it didn't work showing an
error,saying "One atom not present in the coupling group". Shall I try to
include MG in Water_ions group via make_ndx ?
Neeru
neeru
neeru sharma wrote:
Thanks Justin.
I tried the simulation with Protein_GDP and Water_ions, considering that
"Water_and_ions" group will include MG. But it didn't work showing an
error,saying "One atom not present in the coupling group". Shall I try
to include MG in Water_ions group via ma
Hi
I want to calculate the standard deviation of SASA of each residue of a
peptide. When using -or option for complete peptide in g_sas we get residue
vs sasa only. So i tried by creating an index file for each residue
separately (residue1.ndx, residue2.ndx and so forth) and then by
calculating by
Hi Jernej,
You can copy the charmm27.ff directory to your working directory and make
changes locally.
Cheers,
Tsjerk
On Dec 14, 2011 2:54 AM, "Jernej Zidar" wrote:
Hi Mark.
>> How will pdb2gmx "know" it has to parse the monomeres.rtp file?
>It can't. You must add to an existing .rtp file.
Th
On 14/12/2011 12:53 PM, Jernej Zidar wrote:
Hi Mark.
How will pdb2gmx "know" it has to parse the monomeres.rtp file?
It can't. You must add to an existing .rtp file.
That's a problem (and a negative surprise), because I can't just add a
new residue to the aminoacids.rtp in Charmm27.ff folder.
On 14/12/2011 4:01 PM, Harpreet Basra wrote:
Hi
I want to calculate the standard deviation of SASA of each residue of
a peptide. When using -or option for complete peptide in g_sas we get
residue vs sasa only.
I don't follow what result you are describing as unsuitable for you needs.
So i tr
Hi Justin.
I am now trying to generate all the missing files (.rtp, .hdb, .tdb,
.atp). I will present the monomeres as aminoacids. Since the polymer
will be simulated along with a lipid membrane (CHARMM36 force field),
I won't actually need the aminoacids.
I have five different monomers (3 + 2
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