Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-15 Thread Ahmet yıldırım
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-15 Thread Justin Lemkul
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-15 Thread Ahmet yıldırım
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-15 Thread Justin Lemkul
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-15 Thread Ahmet yıldırım
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 =

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-15 Thread Justin Lemkul
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 =

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Justin Lemkul
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Ahmet yıldırım
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,

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Justin Lemkul
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Ahmet yıldırım
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Justin Lemkul
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Ahmet yıldırım
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.

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Justin Lemkul
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Ahmet yıldırım
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

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-11 Thread Justin Lemkul
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

[gmx-users] tip5p water model:Atomtype LP1 not found

2013-04-10 Thread Ahmet yıldırım
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 ] ;