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Today's Topics:
1. selenomethionine parameters for ffG53a6 (Deniz KARASU)
2. Re: Tabulated potentials and performance (Lanyuan Lu)
3. Heme_Grompp Error (shahid nayeem)
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Jul 2010 22:24:13 +0300
From: Deniz KARASU <[email protected]>
Subject: [gmx-users] selenomethionine parameters for ffG53a6
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
Where can I find selenomethionine parameters for ffG53a6 forcefield?
Deniz.
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Message: 2
Date: Mon, 19 Jul 2010 17:18:02 -0500
From: Lanyuan Lu <[email protected]>
Subject: Re: [gmx-users] Tabulated potentials and performance
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="utf-8"
From our group's experience, there is a critical point for dramatic
performance drop when one uses two many tables. The possible reason is
that
the size of tables exceeds the cache size. However, this only happens when
the number of tables is beyond something like 50. The total table size for
the critical point can depend on the hardware condition.
Lanyuan
On Mon, Jul 19, 2010 at 1:49 PM, ms <[email protected]> wrote:
On 19/07/10 18:32, Da-Wei Li wrote:
I remember the manu states that it won't cost too much compared with
standard potential function form.
Well, I find in the manual exactly the opposite:
"Note that table lookup is signiï¬cantly slower than computation of the
most
simple Lennard-Jones and Coulomb interaction." (p.133)
But I am already using tables for most nonbonded interactions and the
performance is OK. What I would like to know is, if I increase the
*number
of tables* (keeping the number of particles/interactions the same, but,
say,
using two tables where I used only one before), is it going to be
significantly worse or not?
thanks!
m.
dawei
On Mon, Jul 19, 2010 at 1:22 PM, ms<[email protected]> wrote:
On 19/07/10 17:32, Da-Wei Li wrote:
It will be very little from my experience. Remember that the dominate
part is the non-bonded force calculation.
Well, that's exactly what I tabulate.
dawei
On Mon, Jul 19, 2010 at 12:22 PM, ms<[email protected]> wrote:
Hi,
Do you know where can I find some information on how using tabulated
potential affects gmx performance, and how? I have to decide how to
project
a custom model but I don't want to calculate dozens of tables only to
find
that gmx grinds to a halt.
thanks!
M.
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Message: 3
Date: Tue, 20 Jul 2010 09:41:56 +0530
From: shahid nayeem <[email protected]>
Subject: [gmx-users] Heme_Grompp Error
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
grompp gives following error.processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations
ERROR 1 [file seq.top, line 1965]:
No default G96Bond types
ERROR 2 [file seq.top, line 5271]:
No default G96Angle types
ERROR 3 [file seq.top, line 5272]:
No default G96Angle types
ERROR 4 [file seq.top, line 5648]:
No default G96Angle types
ERROR 5 [file seq.top, line 5653]:
No default G96Angle types
ERROR 6 [file seq.top, line 5654]:
No default G96Angle types
ERROR 7 [file seq.top, line 5655]:
No default G96Angle types
ERROR 8 [file seq.top, line 5656]:
No default G96Angle types
ERROR 9 [file seq.top, line 6201]:
No default Proper Dih. types
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file seq.top, line 6932]:
System has non-zero total charge: 7.000001e+00
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
There was 1 note
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986
Fatal error:
There were 9 errors in input file(s)
-------------------------------------------------------
pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of
heme porphyrins. It is actually these six bond which is created in
topology
file with pdb2gmx using specbond.dat, giving error in grompp. I tried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these
bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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