[gmx-users] High Temperatures in NVT

Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something wrong with the system or is this normal to see such fluctuations ? There was no warning and the

[gmx-users] RE: polymer duplicate atoms

Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue

[gmx-users] Re: polymer duplicate atoms

Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue

[gmx-users] implicit solvation

hi, I am trying to simulate a 50 residue protein in implicit water.Can anyone tell me that why we usually set the cuttoff to be 0. coulombtype = Cut-off vdwtype = Cut-off nstype = grid nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0. I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you

Re: [gmx-users] High Temperatures in NVT

What happens when you take a children's swing in the playground, place it in some crazy position and push it off in some random direction? The swing will swing, but it won't look proper for a while. Apparently your initial conditions are a bit crazy, e.g. some void next to your solute where a

Re: [gmx-users] implicit solvation

On Fri, Mar 15, 2013 at 9:28 AM, preetichoudh...@iisermohali.ac.in wrote: hi, I am trying to simulate a 50 residue protein in implicit water.Can anyone tell me that why we usually set the cuttoff to be 0. See pbc = no in chapter 7. coulombtype = Cut-off vdwtype = Cut-off nstype = grid

Re: [gmx-users] High Temperatures in NVT

Thanks for replying Mark So in that case, i presume a proper npt run should indicate all is well with the system. Since there was nothing wrong in the output .gro file of nvt and also the npt run was alright , should i go ahead with the production run ? Abhishek What happens when you take a

Re: [gmx-users] High Temperatures in NVT

A single frame proves very little. You should be looking at the trends in (say) average values in observables relevant to what you're going to want the simulation to sample. It's a bit of a dark art, however. Mark On Fri, Mar 15, 2013 at 11:02 AM, Abhishek Acharya aacha...@iitk.ac.inwrote:

Fw: Fwd: [gmx-users] position restraints

Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible?

Re: Fwd: Fw: Fwd: [gmx-users] position restraints

I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include

[gmx-users] Dihedral restraints in 4.6 vs 4.5.X

Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5

[gmx-users] Error Quick and Dirty installation

Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and dirty installation I have this errors: [ 1%] Performing download step (download, verify and extract) for 'gmxfftw' -- downloading... src='http://www.fftw.org/fftw-3.3.2.tar.gz'

[gmx-users] Timesteps don't match

Dear all, I'm receiving a timesteps don't match error, due to a wobble in the time between steps for my xtc trajectory file. The source of the wobble is mysterious. I'm running gromacs-4.5.5 with plumed patches for a very long trajectory using double precision code with a time step of 2fs and

[gmx-users] Treating electrostatics and van der Waals interactions differently

Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics calculation but I would like to exclude 1-2 and 1-3

Re: [gmx-users] Error Quick and Dirty installation

That means the automatic download of FFTW did not succeed for some reason. GROMACS is not going to compile an FFTW for you unless it's sure the FFTW download was complete and the right file. Either do make clean and try again, or follow the other build instructions to prepare a suitable FFTW for

Re: [gmx-users] Treating electrostatics and van der Waals interactions differently

On 2013-03-15 19:27, Jeff Woodford wrote: Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics

Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X

On 2013-03-15 15:31, Per Larsson wrote: Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral

Re: [gmx-users] Treating electrostatics and van der Waals interactions differently

On Fri, Mar 15, 2013 at 7:27 PM, Jeff Woodford jwoodf...@missouriwestern.edu wrote: Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all

Re: Fw: Fwd: [gmx-users] position restraints

On 3/15/13 8:50 AM, Shima Arasteh wrote: Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints.

Re: Fwd: Fw: Fwd: [gmx-users] position restraints

On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE

[gmx-users] Treating electrostatics and van der Waals interactions differently

Looking into the manual, i find under the 'energy monitor group': 'Mutual interactions between all energy monitor groups are compiled during the simulation. This is done separately for Lennard-Jones and Coulomb terms. In principle up to 256 groups could be defined, but that would lead to

[gmx-users] Parallelization performance

Hi! I have been running MD simulations on a 6 processors machine. I just got an account on a cluster. A nvt stabilization takes about 8 hours on my 6 processors machine, but it takes about 12 hours on the cluster using 16 processors. It is my understanding that the idea of running in parallel is