[gmx-users] do_dssp for coarse-grained trajectory

Dear All, I have a trajectory with the protein represented by C-Alpha atoms only. I was wondering if I could use ' do_dssp ' for predicting the secondary structure for this trajectory. When I tried to do so ( do_dssp -f trajca.xtc -s reference.pdb -o dssp_traj ) I got the following error - F

Re: [gmx-users] calculating free energy

  In general a realistic unfolded system would have to start at several random points in state A, and allowing it to fold into state B.  This accounts for gaussian distributions of random states... these tend to be long as the folding process is between 200 (for short) to 5-6 usecounds for longe

Re: [gmx-users] CH3CN solvents breaking the periodic box

Thanks Justin for your valuable answer.. -Original Message- From: "Justin Lemkul" Sent: ‎4/‎19/‎2015 8:48 PM To: "gmx-us...@gromacs.org" Subject: Re: [gmx-users] CH3CN solvents breaking the periodic box On 4/18/15 2:33 AM, Debashis Sahu wrote: > Dear Gromacs users, >

Re: [gmx-users] Constraints applied for keeping rigid in ND

Hang, This is exactly the problem. Your system isn't set up properly, and you are trying to mask this fact behind constraints. By the way, oscillatory behavior does not necessarily mean the system is too soft. It may actually mean that your set of connstants is causing resonant or near-resonan

Re: [gmx-users] Constraints applied for keeping rigid in ND

Hi Hang, Are the angles in the system conserved via artificial bonds? In other words, when you run your diamond, does it lose crystal shape, or does it stay diamond? I am just trying to understand what you call "soft". You can always try SHAKE instead of LINCS, if you insist on constraints, i'm ju

Re: [gmx-users] Constraints applied for keeping rigid in ND

Hi Alex, Thanks for your reply. I used large time step because it is the default value(20 ~40 ps) for the Martini Coarse Grained ff. Applied that large time step, the angles and bonds have been proved that they could not keep ND rigid enough. And for a very large system I want to build in future,

Re: [gmx-users] Constraints applied for keeping rigid in ND

Also, I just looked at your topology. Where are your angles? Try to implement them and then turn off constraints. Alex A> Is there a particular reason you're applying LINCS constraints to your A> diamond structure? Usually, LINCS gives convergence A> errors/warnings if the system is poorly A> eq

Re: [gmx-users] Constraints applied for keeping rigid in ND

Is there a particular reason you're applying LINCS constraints to your diamond structure? Usually, LINCS gives convergence errors/warnings if the system is poorly equilibrated and/or your time step is too large. The fact that your system was "soft" without constraints actually suggests poor setup,

[gmx-users] Constraints applied for keeping rigid in ND

Hi all, My research focuses on the dynamics of a nanodiamond(ND) in a biological environment. I am working with gromacs version 5.0.2 and using Martini CG ff. In order to keep the rigidity of ND, I applied constraints as the stiff bond in the .itp file. But my system crashed in the NVT run with LI

Re: [gmx-users] g_wham error in umbrella simulation

On 4/19/15 9:53 PM, Ming Tang wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respect

Re: [gmx-users] g_wham error in umbrella simulation

Dear Mr. Kortzak, I had same problems. There could be many reasons, but in my case, I had some uncompleted jobs. For instance, umbrella137 could be terminated abnormally but you can have tpr, log and xvg which are generated from uncompleted job. Why don’t you check the results? Regards Yoo

Re: [gmx-users] g_wham error in umbrella simulation

Thanks for your advice. I just checked. There is no empty line at the end of the .dat files. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Kortzak, Daniel Sent: Monday, 20 April 2015 8:01

[gmx-users] g_wham error in umbrella simulation

Maybe some empty lines at the end of your .dat files. Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.

[gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Dear Gromacs users I am trying to pull a drug molecule across the plasma membrane, from one side to the another side of the membrane. But when I am using pull_geometry= position, it's giving error, as I found that this option is removed in the gromacs 5.0.4. So I am using pull_geometry = dista

Re: [gmx-users] help: Gromacs

Hi, What hardware to buy for GROMACS also depends a bit on what kind of MD simulations you intend to run on it (how big? one single simulation or lots of smaller ones?), and of course on how much money you can invest. The two choices you provide are very different in price; the more expensive