[gmx-users] Normal Mode

is of course good. However, I am getting 16 eigenfrequencies from 5000 to 21,000 cm-1 with enormous eigenvalues. This does not appear correct. Any insights as to why gromacs is producing these would be appreciated. Dan Sponseller PhD candidate George Mason University. -- Gromacs Users mail

[gmx-users] Normal Mode Analysis

Hello. I am trying to do a Normal Mode Analysis of a polymer in water. I am running my minimization right now with -DFLEXIBLE defined. How do I exclude the water from the analysis. I only want the analysis done on the polymer. Dan Sponseller PhD student, George Mason University -- Gromacs

Re: [gmx-users] editconf -density

You do not state your original density. But lets say you need to reduce volume 3% to get your correct density. Use: ediftconf -f solv_large.gro -o solv_large_scaled.gro -scale 1 1 0.97 Just do a quick side calculation for what you need and substitute in for 0.97. Dan > On Aug 9, 2015, at 4:18

[gmx-users] Help me with energy groups please.

figure this out please. Attached is my mdp file. Dan Sponseller ** Run Control ** integrator = steep nsteps = 1 comm-mode= Linear nstcomm = 100 ** Energy Minimization emtol= 0.001 emstep

Re: [gmx-users] all in one pc for MD simulation calculations

Hello. You do not provide enough detail for any type of answer. For example. I have run a small molecule (100 atoms) on my laptop and finished in an hour. I am currently running 7 atoms on a computing cluster with 128 CPUs and it will take a week or two. Dan George Mason University > O

[gmx-users] Morse potential conversion.

Hello GMX list. I am using the morse potential and I know that grompp converts the bonds from the harmonic potential to the morse potential at that time. From the equations 4.39 to 4.44 in the gromacs 5 manual, I can safely conclude that the bottom of the well is defined at Vm=0.0 so that with

Re: [gmx-users] Build-Gromacs installation error

You might not have MPI installed on your computer (or MPICH). However, sounds like you are installing this on a personal computer. You should turn off MPI as GROMACS’ internal thread MPI is excellent. You only need to turn on MPI if you are installing this on a cluster where multiple CPUs are us

Re: [gmx-users] Jump in temperature each time a new simulation is started.

-seed = 4242 ** Bonds ** constraints = none morse= yes > On Dec 31, 2014, at 3:07 PM, Justin Lemkul wrote: > > > > On 12/31/14 3:05 PM, Dan Sponseller wrote: >> Hello. >> >> Every time I start a new si

[gmx-users] Jump in temperature each time a new simulation is started.

Hello. Every time I start a new simulation from a conformation that has been well equilibrated, there is a jump in the temperature. For example, starting from a .gro file with velocities that was a well equilibrated system at 400K has initial temperature about 440K. I am not generating new vel

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

estimate on your pressure is 6.2. That could put your actual pressure at 1. Dan Sponseller PhD student George Mason University > On Oct 30, 2014, at 1:49 AM, Agnivo Gosai wrote: > > Dear Users > > I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS > 4.5.

[gmx-users] Bond Energy question.

step zero, should not the bond energy not have changed? The G96Bond energy should just be reporting the interaction between bonded atoms, correct? Thanks for any insight. Dan Sponseller PhD student George Mason University -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Positive Potential Energy.

Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation

Re: [gmx-users] Gromacs 5.0 installation

Hello. Just take the .tar.gz on a thumb drive to your new machine and install from that. Note that this machine will already need to have all the prerequisites. If not, you will need to install those first: cmake gcc Don’t forget fftw lapack and blas. You can use the ones built in gromacs with

[gmx-users] Difficulty preparing a polymer (PEG) for simulation

Snip from ‘merged.rtp’ ;Dan Sponseller ;Copying from DME below for the repeating chain for PEG. [ LIG ] [ atoms ] C1 CC32A -0.010 0 H11 HCA2A0.090 1 H12 HCA2A0.090 2 OO2 OC30A -0.340 3 C3 CC32A -0.010 4 H31 HCA2A0.090 5

[gmx-users] Difficulty preparing a polymer (PEG) for simulation.

Snip from ‘merged.rtp’ ;Dan Sponseller ;Copying from DME below for the repeating chain for PEG. [ LIG ] [ atoms ] C1 CC32A -0.010 0 H11 HCA2A0.090 1 H12 HCA2A0.090 2 OO2 OC30A -0.340 3 C3 CC32A -0.010 4 H31