I edited the grompp output and sent it to you. Bring that again here:
Generated 21528 of the 21528 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 18355 of the 21528 1-4 parameter combinations
ERROR 1 [file topol.top, line 414]:
No default Bond types
On 31/07/2012 7:16 AM, Shima Arasteh wrote:
Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-)
I regenerated the topol.top to check the correctness of input and FF files.
Some output has been changed however a little bit. Now, I bring you all was
needed again:
1. rtp en
On 7/30/12 5:15 PM, sai nitin wrote:
Dear all,
I recently started protein ligand simulation using gromacs my aim is
to calculate binding free energies after simulations...I adapted
justin tutorial
and done 10 ns MD simulations using CHARMM FF and now going through
LIE (Linear Interaction Ener
On 7/30/12 1:07 PM, vidhya sankar wrote:
Dear Justin, Thank you for your Previous Reply.
I have got the following Error in EM using steepest
Descent method in gromacs
Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is
larger than the 1-4 table s
Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-)
I regenerated the topol.top to check the correctness of input and FF files.
Some output has been changed however a little bit. Now, I bring you all was
needed again:
> 1. rtp entry
>
>[ FVAL ]
[ atoms ]
CN C 0.
Dear all,
I recently started protein ligand simulation using gromacs my aim is
to calculate binding free energies after simulations...I adapted
justin tutorial
and done 10 ns MD simulations using CHARMM FF and now going through
LIE (Linear Interaction Energie method) g_lie in gromacs..
And came
Dear Justin, Thank you for your Previous Reply.
I have got the following Error in EM using steepest
Descent method in gromacs
Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is
larger than the 1-4 table size 3.000 nm
These are ignored for the rest o
On 30/07/2012 8:49 PM, Shima Arasteh wrote:
If you want further help, you will need to paste your .rtp entry(s), the
N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx
output, the N-terminal fragment of the grompp -c input, grompp >command line,
and full grom
Thank you M.ark..
I got following reply..
Fatal error :
mdrun -multi is not supported with thread library .Please compile
gromacs with MPI support.
I have to try to compile gromacs as per the webpage instructions...
With best wishes and regards..
Rama David..
--
gmx-users mailing listgmx-u
On 30/07/2012 8:34 PM, rama david wrote:
thank you for immediate reply...
Suppose, If I installed from Fedora software packages
How to check that Gromacs installed in Parallel version and can
performed REMD
Make topol0.tpr and topol1.tpr as copies of the same .tpr file, and run
mpirun mdr
>If you want further help, you will need to paste your .rtp entry(s), the
>N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full
>pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp
>>command line, and full grompp output. You may think your context is cl
thank you for immediate reply...
Suppose, If I installed from Fedora software packages
How to check that Gromacs installed in Parallel version and can
performed REMD
Thank you in Advance..
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-user
On 7/30/12 5:55 AM, Za Pour wrote:
Dear gmx users
I am trying to analyze the results of my simulations. a system
including one CNT+12 small molecules.I would like to know the distribution
of angles formed by these 12 small molecules around CNT.I have found from
manual that
g_sgangle may do th
Dear gmx users
I am trying to analyze the results of my simulations. a system
including one CNT+12 small molecules.I would like to know the distribution
of angles formed by these 12 small molecules around CNT.I have found from
manual that
g_sgangle may do that however, in the manual has been sai
On 30/07/2012 7:41 PM, Shima Arasteh wrote:
You are right, CT1 is incorrect for sure. But the other option is C(carbonyl
C) . Maybe I couldn't say it clearly.
The FVAL which I sent before through mailing list, is the result of this
formamide and the CGenff generation:
[ FVAL ]
[ atoms
You are right, CT1 is incorrect for sure. But the other option is C(carbonyl
C) . Maybe I couldn't say it clearly.
The FVAL which I sent before through mailing list, is the result of this
formamide and the CGenff generation:
[ FVAL ]
>> [ atoms ]
>> CN C 0.357 0
>>
On 30/07/2012 7:11 PM, Shima Arasteh wrote:
In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of
formyl group ( as you see earlier)
No, I saw atom types chosen that included wrong things like CT1. If
you're happy that you're using atom types that belong in formyl, then g
On 30/07/2012 6:56 PM, rama david wrote:
Hi GROMACS FRIENDS,
I have dell T3500 precision, 64 bits, 6C workstation with fedora
operating system.
I want to install gromacs in parallel mode with mpi...
I am planning to performed Replica Exchange Molecular Dynamics ( REMD ).
As per REMD instru
In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of
formyl group ( as you see earlier) . If I don't use these, so what atom types?!
I sent an email to Prof.Roux the author of this article
http://www.pnas.org/content/101/1/117.abstract . He suggested me to use the
parameter
If you install package 1 on your list, the second one will be
installed as well (ie you need both of them).
// Linus
On Mon, Jul 30, 2012 at 10:56 AM, rama david wrote:
> Hi GROMACS FRIENDS,
> I have dell T3500 precision, 64 bits, 6C workstation with fedora
> operating system.
> I want to
Hi GROMACS FRIENDS,
I have dell T3500 precision, 64 bits, 6C workstation with fedora
operating system.
I want to install gromacs in parallel mode with mpi...
I am planning to performed Replica Exchange Molecular Dynamics ( REMD ).
As per REMD instruction
http://www.gromacs.org/Documentation/H
On 30/07/2012 6:36 PM, Shima Arasteh wrote:
Thanks dear Mark.
Actually the atomtype C is more suitable for C atom of formyl and not CT1!
The same as before I get the no default bonds/angles/dihedral errors . You
explained what I am suppose.
I can understand the way of matching the coordinate fi
Thanks dear Mark.
Actually the atomtype C is more suitable for C atom of formyl and not CT1!
The same as before I get the no default bonds/angles/dihedral errors . You
explained what I am suppose.
I can understand the way of matching the coordinate file and atom types in .rtp
file. But it's not
Dear Mark,
Thank you for your reply.
I have read the documentations from
http://www.gromacs.org/Documentation/Installation_Instructions/GPUs and also,
from gromacs manual. I configured my system strictly followed by the
instruction from it.
My GPU is GTX-480, which is supported by gromacs.
Th
Dear Mark,
Thank you for your reply.
I have read the documentations from
http://www.gromacs.org/Documentation/Installation_Instructions/GPUs and also,
from gromacs manual. I configured my system strictly followed by the
instruction from it.
My GPU is GTX-480, which is supported by gromacs.
T
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