I have the following files in directory
1.tip5p.gro
2.topol.top
3.em.mdp
topol.top:
#include oplsaa.ff/forcefield.itp
#include oplsaa.ff/tip5p.itp
[ system ]
water
[ molecules ]
SOL 512
commands:
editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0
genbox -cp protein-PBC.gro -cs
On 4/15/13 6:58 AM, Ahmet yıldırım wrote:
I have the following files in directory
1.tip5p.gro
2.topol.top
3.em.mdp
topol.top:
#include oplsaa.ff/forcefield.itp
#include oplsaa.ff/tip5p.itp
[ system ]
water
[ molecules ]
SOL 512
commands:
editconf -f tip5p.gro -o protein-PBC.gro -bt cubic
I did as you said. I corrected number of water molecules in the topology by
hand.
grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
protein-water.tpr
Steepest Descents converged to Fmax 1000 in 3 steps
Potential Energy = -1.5700267e+05
Maximum force = 7.2195142e+02 on atom 3761
On 4/15/13 7:22 AM, Ahmet yıldırım wrote:
I did as you said. I corrected number of water molecules in the topology by
hand.
grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
protein-water.tpr
Steepest Descents converged to Fmax 1000 in 3 steps
Potential Energy = -1.5700267e+05
The norm of force is very high. And the system converged in 3 steps
For example, I got the following results for spc water model
Steepest Descents converged to Fmax 1000 in 167 steps
Potential Energy = -2.1208019e+05
Maximum force = 9.8452704e+02 on atom 286
Norm of force =
On 4/15/13 8:28 AM, Ahmet yıldırım wrote:
The norm of force is very high. And the system converged in 3 steps
For example, I got the following results for spc water model
Steepest Descents converged to Fmax 1000 in 167 steps
Potential Energy = -2.1208019e+05
Maximum force =
On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear users,
I am trying MD simulation of tip5p water model. I am getting Fatal
Error:Atomtype LP1 not found.
There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2
atoms in atomtypes.atp file?
(I
Dear Justin,
I copied to gmx.ff it. You know the tip5p shows the general shape of the
5-site water models but the spc shows the general shape of the 3-site water
models. Therefore I need tip5p.itp.
How can you get it?
2013/4/11 Justin Lemkul jalem...@vt.edu
On Thu, Apr 11, 2013 at 1:56 AM,
On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear Justin,
I copied to gmx.ff it. You know the tip5p shows the general shape of the
5-site water models but the spc shows the general shape of the 3-site water
models. Therefore I need tip5p.itp.
Is there going to
I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from
gromacs 4.0.7. are they wrong?
2013/4/11 Justin Lemkul jalem...@vt.edu
On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com
wrote:
Dear Justin,
I copied to gmx.ff it. You know the tip5p shows the
On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from
gromacs 4.0.7. are they wrong?
Well, they trigger a fatal error...
Yes, they are wrong and newer versions of Gromacs are correct.
-Justin
There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt
find them
2013/4/11 Justin Lemkul jalem...@vt.edu
On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com
wrote:
I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from
gromacs 4.0.7.
On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt
find them
They're there. The tip5p.gro file is in $GMXLIB and tip5p.itp is in several
force field subdirectories.
$ ls -l *.ff/tip5p.itp
I am simulating tip5p water. I got tip5p.gro from $GMXLIB
1.) editconf -f tip5p.gro -o protein.pdb
2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top
14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals))
Select the Water Model:
1: TIP4P TIP 4-point, recommended
2: TIP3P TIP
On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
I am simulating tip5p water. I got tip5p.gro from $GMXLIB
1.) editconf -f tip5p.gro -o protein.pdb
2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top
14 (OPLS-AA/L all-atom force field (2001 aminoacid
Dear users,
I am trying MD simulation of tip5p water model. I am getting Fatal
Error:Atomtype LP1 not found.
There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2
atoms in atomtypes.atp file?
(I am using Gromacs 4.5.5)
usr/share/gromacs/top/gmx.ff/tip5p.itp
...
[ atoms ]
;
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