Re: [gmx-users] LINCS warning in md run

2012-09-20 Thread reisingere
Hi Justin, thank you a lot for your answer. I will try it. Best, Eva > > > On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi, >> now I tried it without any restriction and still the LINCS warnings >> occur. >> Since it is always the hydrogen atom where the huge force

Re: [gmx-users] LINCS warning in md run

2012-09-20 Thread Justin Lemkul
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another

Re: [gmx-users] LINCS warning in md run

2012-09-20 Thread reisingere
Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And ind

Re: [gmx-users] LINCS warning in md run

2012-09-18 Thread Justin Lemkul
On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey, now I tried it without any fixed residues. But still the energy after the minimization is not very low and I still get the LINCS warnings. The mdp file I use for the minimization looks like this: define

Re: [gmx-users] LINCS warning in md run

2012-09-18 Thread reisingere
Okey, now I tried it without any fixed residues. But still the energy after the minimization is not very low and I still get the LINCS warnings. The mdp file I use for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 1

Re: [gmx-users] LINCS warning in md run

2012-09-18 Thread Justin Lemkul
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. Another thing worth considering - why do you necessarily need the rest of the structure to be identical? Or perhaps

Re: [gmx-users] LINCS warning in md run

2012-09-18 Thread Peter C. Lai
Looks like there is still something clashing with atom 979. The resulting force after EM was close to 1, which is not very much minimized at all... What is atom 979 and what is near it? On 2012-09-18 01:22:25PM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: > I need the rest of t

Re: [gmx-users] LINCS warning in md run

2012-09-18 Thread Justin Lemkul
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of

Re: [gmx-users] LINCS warning in md run

2012-09-18 Thread reisingere
I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. I just added the phosphate manually and so I want to minimize and run a short MD with it. I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryc

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread Justin Lemkul
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md ru

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread reisingere
Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minim

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread Justin Lemkul
On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? Visualization. This is the topology for this residue in the aminoacid.rtp file. I added it ma

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread reisingere
Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? This is the topology for this residue in the aminoacid.rtp file. I added it manually. The parameter are from the amber parameter database (http://www.pharmacy.manchester.ac.

Re: [gmx-users] LINCS warning in md run

2012-09-12 Thread Justin Lemkul
On 9/12/12 3:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout

Re: [gmx-users] LINCS warning in md run

2012-09-12 Thread reisingere
Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy

Re: [gmx-users] LINCS warning in md run

2012-09-12 Thread Justin Lemkul
On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example: Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979) bon

[gmx-users] LINCS warning in md run

2012-09-12 Thread reisingere
Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example: Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, curre