Re: [gmx-users] Switching off electorstaic

On 08/10/17 04:12, atanu das wrote: Hi, I am intending to run a simulation of a protein in 100 nM NaCl solution by turning off protein's electrostatic interactions, but keeping the LJ alive, so that water and salt behave as usual and the protein only behaves as a hydrophobic polymer chain. The

[gmx-users] Equilibration using position restraints in NPT

This is a very common post on previous mailing list however, I am still not able to fix the problem of position restraints during NPT. I have a carbon nanotube aligned to z-direction. I am trying to simulate infinite nanotube using periodic conditions. It is common to use position restraints for n

[gmx-users] Regarding charges for atoms in a molecule

Hello, I have an amino-acid (eg. glycine) and water mixture, and by using charmm36 ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o abc.gro command. 1] In the topology file, the charges for each atom are assigned. from where are these charges assigned..?? is it from the .rtp

Re: [gmx-users] Regarding charges for atoms in a molecule

On 10/8/17 1:04 PM, Dilip H N wrote: Hello, I have an amino-acid (eg. glycine) and water mixture, and by using charmm36 ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o abc.gro command. 1] In the topology file, the charges for each atom are assigned. from where are these

Re: [gmx-users] Equilibration using position restraints in NPT

Hi, The simplest explanation is that your box size is inappropriate for the contents. If the box wants to change size but the nanotube is restrained to fixed positions then you have an invalid model. Mark On Sun, 8 Oct 2017 15:39 Neha Gandhi wrote: > This is a very common post on previous mail

[gmx-users] Equilibration using position restraints in NPT

Thank you Mark. The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and solvate using spc216.gro. How can I calculate box size after NVT so that I get density of 1 or 0.99 when using pressure coupling? > Message: 1 > Date: Sun, 8 Oct 2017 23:38:58 +1000 > From: Neha Gandhi

Re: [gmx-users] Equilibration using position restraints in NPT

PBC for crystals are not set this way, this is why the simulator is turning the CNT into a pogo stick. Prior to any simulations, please calculate the correct PBC-compatible axial length using crystallographic considerations and CNT chirality, -box properly, generate topology with PBC, then pro

Re: [gmx-users] Equilibration using position restraints in NPT

In addition, the CNT edges have to be periodically commensurate. On 10/8/2017 3:36 PM, Alex wrote: PBC for crystals are not set this way, this is why the simulator is turning the CNT into a pogo stick. Prior to any simulations, please calculate the correct PBC-compatible axial length using c

[gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

Dear list, I have gone through carbon nanotube guide on GROMACS website. http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube I have a nanotube aligned to z-direction. I am trying t

Re: [gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

I just replied to Neha's post. You are having issues that have nothing to do with Gromacs, i.e. Gromacs is simply responding to incorrect system setup. Please generate a proper periodic topology and use a PBC-compatible box. Alex On 10/8/2017 3:47 PM, Ming Tang wrote: Dear list, I have gon

Re: [gmx-users] Equilibration using position restraints in NPT

On Sun, Oct 8, 2017 at 11:30 PM Neha Gandhi wrote: > Thank you Mark. > > The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and > solvate using spc216.gro. > Please visualize that result. Such a command would put solvent all around your nanotube, so it could not have an infin

Re: [gmx-users] No performance increase with single vs multiple nodes

Hi, On Sun, Oct 8, 2017 at 2:40 AM Matthew W Hanley wrote: > I am running gromacs 2016.3 on CentOS 7.3 with the following command using > a PBS scheduler: > > > #PBS -N TEST > > #PBS -l nodes=1:ppn=32 > > export OMP_NUM_THREADS=1 > > mpirun -N 32 mdrun_mpi -deffnm TEST -dlb yes -pin on -nsteps