yes, the ions I have can be considered as bound. I found out I also had to
declare the type of residue as "Ion" in file residues.dat :)
On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul wrote:
>
>
> On 6/23/17 3:50 PM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I'm trying to add a new ty
On 6/23/17 3:50 PM, Jose Borreguero wrote:
Dear Gromacs users,
I'm trying to add a new type of atom as an ion. Looking at already existing
ions, such as sodium (NA), I see there's an entry both in files ions.itp
and aminoacids.rtp. My question is, what is the rationale of declaring ions
both a
If you want the ion to be recognized as an individual residue, you need to
stick it in the *.rtp file.
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
___
Dear Gromacs users,
I'm trying to add a new type of atom as an ion. Looking at already existing
ions, such as sodium (NA), I see there's an entry both in files ions.itp
and aminoacids.rtp. My question is, what is the rationale of declaring ions
both as ions and as residues? Is this always required
Dear sir i have force field for O2 now some one work over it before its the
.prm file he use to run simulation amber99 force field and use there own
lab heme generated ff heme fe 02 now how i can use these amber heme
force field in Gromacs thanks.
On Fri, Jun 16, 2017 at 3:23 AM, Mark Abraham
Hi,
Once you've compiled GROMACS for this machine (will run at least twice as
fast), your setup is likely optimal. The options and what to do with them
are all in the 5.1 gromacs user guide online.
Mark
On Fri, 23 Jun 2017 16:10 Sergio Manzetti
wrote:
> Hi, I have the following system:
>
> Run
Hi,
And follow the advice of the Martini authors for using the Verlet scheme
with their forcefield.
Mark
On Fri, 23 Jun 2017 17:20 Justin Lemkul wrote:
>
>
> On 6/23/17 11:08 AM, Alex Mathew wrote:
> > Dear all,
> >
> > While running CGMD in GPU i got this error
> >
> > OpenMP threads have bee
Thank you for the clarification!
-Angela
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Alex
Sent: June 22, 2017 7:57 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Constraint vs. Umbrella in Pull COM
In the case of
On 6/23/17 10:04 AM, Sergio Manzetti wrote:
Hi, I have the following system:
Running on 1 node with total 24 cores, 24 logical cores
Hardware detected:
CPU info:
Vendor: AuthenticAMD
Brand: AMD Opteron(tm) Processor 6344
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD inst
On 6/23/17 10:26 AM, Alex Mathew wrote:
Dear all,
I was wondering the analysis we usually use in the all-atom simulation will
work in for CG model?
I guess secondary structural analysis will be useless since it's not
considering all atoms. What about non-bonded energies and other parameters
suc
On 6/23/17 11:08 AM, Alex Mathew wrote:
Dear all,
While running CGMD in GPU i got this error
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet
Here can i change the cut-off scheme to Verlet ?
Amazingly enough:
cutoff-sche
Hi all,
I am reading the paper "Replica-exchange molecular dynamics method for
protein folding" by Yuko Okamoto. In this paper, they exchange temperatures
of 2 replica. To evaluate that replica exchange is successful, they
calculate exchange probability; plot the temperature, potential energy per
r
Dear all,
While running CGMD in GPU i got this error
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet
Here can i change the cut-off scheme to Verlet ?
ff is martini22p
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Gromacs Users mailing list
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Hello,
I am recompiling GROMACS on a new compute node and I am getting a unit test
failure (shown below). I am compiling with GNU 4.8.5 and the following
cmake commands:
cmake .. -DCMAKE_INSTALL_PREFIX=[redacted] -DGMX_MPI=on -DGMX_GPU=off
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX
Dear all,
I was wondering the analysis we usually use in the all-atom simulation will
work in for CG model?
I guess secondary structural analysis will be useless since it's not
considering all atoms. What about non-bonded energies and other parameters
such hydrogen bond and essential dynamics?
Than
Hi, I have the following system:
Running on 1 node with total 24 cores, 24 logical cores
Hardware detected:
CPU info:
Vendor: AuthenticAMD
Brand: AMD Opteron(tm) Processor 6344
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time
The problem has been solved. I forgot to delete some entries when using .top
file as .itp file.
Thanks,
Qing
At 2017-06-23 15:36:32, "Mark Abraham" wrote:
>Hi,
>
>You can't just paste together two topology files intended to stand alone
>e.g. because they have [defaults] sections. You can #inc
At 2017-06-23 21:55:39, "Justin Lemkul" wrote:
>
>
>On 6/23/17 9:53 AM, Qing Lv wrote:
>> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither
>> work...
>
>There is no chain information in a .gro so this approach cannot work. If you
>have a multimeric complex, and you ne
On 6/23/17 9:53 AM, Qing Lv wrote:
I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...
There is no chain information in a .gro so this approach cannot work. If you
have a multimeric complex, and you need to use these weird 5-character names,
process each .gro s
I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...
Qing
At 2017-06-23 17:19:55, "Fitsiou, Eleni" wrote:
>Hi ,
>Rename your chains and you could use -merge interactive and the -ter flag
>Best
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>
>* Please search the archive at
>ht
Thanks, that fixed it!
Sergio Manzetti
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
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Org.nr. 911 659 654
Tlf: +47 57695621
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On 6/23/17 1:02 AM, Dilip H N wrote:
Hello all,
I want to simulate methylamine with amino acid misture in CHARMM FF, so i
have created methylamine in mol2 format and created the .itp and .pdb files
from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have
included it in topology
On 6/23/17 6:20 AM, Sergio Manzetti wrote:
Hi, I Have prepared a box, which just grows beyond proportions in order to
satisfy grompp complaining about the box being less than the double of rlist,
so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box
quickly becomes o
Hi, it seems that there is something with the force field that gives issues:
The same parameters are used for 5 molecules in a test run:
Using AMBER99SB ISTN :
2 of 5 small molecules work perfectly in the simulation in water.
3 of the 5 small molecules stop at grompp MD.mdp step giving the
Hi, I Have prepared a box, which just grows beyond proportions in order to
satisfy grompp complaining about the box being less than the double of rlist,
so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box
quickly becomes over 14x14x14. When one visualizes it one can se
Hi ,
Rename your chains and you could use -merge interactive and the -ter flag
Best
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My protein contains 2 chains, and ILE294 is the C-terminus of chain 1. When I
used pdb2gmx to process the GRO file, it can recognize N-terminus of chain 1
and C-terminus of chain 2, but cannot recognize C-terminus of chain 1. Since
there is no chain separators in GRO files (like "TER" in PDB), p
Dear Mark,
Actually I had tried the method you suggested, but got such errors (pdb2gmx):
Fatal error:
Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while
sorting atoms.
ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are
no atom "O1" or "O2"
Thanks Alex, finding the positions as you propose seems a legitimate way
for this problem. One will have to wait enough with a classical MD but Bias
MD should help. In my case the channel is not a large ion channel.
FR.
2017-06-22 18:26 GMT+02:00 Alex :
> I've never used PLUMED, to be honest, so
Hi,
You can't just paste together two topology files intended to stand alone
e.g. because they have [defaults] sections. You can #include files, but
they have to follow the structure of the example in chapter 5 of the manual
(and every tutorial). Defaults, then atomtypes and parameters, then
molec
Hi,
I suggest you produce your initial conformation in .gro format, which
permits five-character atom names. That might mean using editconf on your
.pdb file, and then manually renaming atoms.
Mark
On Fri, Jun 23, 2017 at 3:55 AM Qing Lv wrote:
> Hi,
>
>
> Gromos 54a7 force field has built-in
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