Re: [gmx-users] trouble minimizing structure with mdrun

Hi Jack, Can you be more specific? A quick glance at 1YQW shows that there's quite a bit of exotic stuff, including several times the infamous Fe4S4 center. How did you deal with that? At first instance, what protocol did you used, and what error did you get (and at which point)? After preparation

[gmx-users] Coordinate output for test particle insertion

Hello everyone.   I'm using the test particle insertion code in gromacs, and I need the coordinates of the particle insertions for some analysis.  Unfortunately, this is not given in any output file so I need to modify the source code.  I've been trying to figure out what I need to change, but I

[gmx-users] trouble minimizing structure with mdrun

I've been having trouble minimizing a structure using gromacs so I decided to try using another MD app and see if I can generate a more relaxed structure. Using VMD & NAMD I was able to minimize and run MD for this structure from RCSB.ORG 1YQW.pdb. It was solvated and ionized. I then took the last

[gmx-users] Dead Link or Restricted Access to link

The links to the videos don't work on this page. Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video 1,video 2,video 3) - (Gerrit Groenhof). http://www.gromacs.org/Documentation/How-tos/QMMM -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

Hello, I recently used mdrun -pd while attempting to solve my problems with angle_restraints_z (http://lists.gromacs.org/pipermail/gmx-users/2010-January/047785.html) since I discovered that -noddcheck is not a valid solution to the missing interactions problems with angle restraints. I

Re: [gmx-users] get 3 roation angles over time

You could use g_principal and follow the change in angles of the three principal axes of your group using simple maths. This might give you what you are looking for. Another way to look at rotations is to use the program DynDom, but this only works on individual structures not trajectories.

Re: [gmx-users] free energy

Nilesh Dhumal wrote: THanks Justin. I am using Groamcs 4.0.7 version. I will do more simulation with more lambada value betwen 0 to 0.1. I really think this is less significant than point #1 I mentioned before. Be sure you are actually setting the relevant .mdp parameters (couple-lambda0,

Re: [gmx-users] free energy

THanks Justin. I am using Groamcs 4.0.7 version. I will do more simulation with more lambada value betwen 0 to 0.1. Thanks. Nilesh On Sun, January 3, 2010 12:39 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hey All, >> I am trying to calculate the solvation free energy of glucose in

Re: [gmx-users] free energy

Nilesh Dhumal wrote: Hey All, I am trying to calculate the solvation free energy of glucose in ionic liquids. I am getting really large value for lamda=0 in vacuum and solvent as well. I am getting final solvation energy value ~ 310 kJ/mol. Can you tell me where I am wrong. There are sever

[gmx-users] free energy

Hey All, I am trying to calculate the solvation free energy of glucose in ionic liquids. I am getting really large value for lamda=0 in vacuum and solvent as well. I am getting final solvation energy value ~ 310 kJ/mol. Can you tell me where I am wrong. Here I have pasted the the lamda value in

Re: [gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

Hi, > Tsjerk gave me suggestion to check the .tpr file created by the command > grompp. I also suggested to try and find out why the water molecules got garbled. Between adding solvent and energy minimization, you also added chloride to counter the net positive charge. I assume you used genion f

[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

Hi Tsjerk gave me suggestion to check the .tpr file created by the command grompp. *Energy minimization of the solvated system* pbc = xyz (minim.mdp) grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated I

Re: [gmx-users] Fwd: What could be wrong with rdf plot?

I am not sure somebody gave you an answer ... the first intense and probably very narrow pick is very likely due to the intramolecular OH distance. It should be around 0.1 nm, isn't it? On Jan 1, 2010, at 3:53 AM, Lum Nforbi wrote: -- Forwarded message -- From: Lum Nforbi D

Re: [gmx-users] Constraints for md simulations of carbohydrates

Neha Bharat Gajaria wrote: Dear List, I want to study the ring puckering of carbohydrates. Is it recommended to use hydrogen-bond constraints or i simply put none in constraints section in the md.mdp file? That depends on the time step you want to use. Refer to the LINCS references provi

[gmx-users] Constraints for md simulations of carbohydrates

Dear List, I want to study the ring puckering of carbohydrates. Is it recommended to use hydrogen-bond constraints or i simply put none in constraints section in the md.mdp file? Many thanks, Regards, Neha Gandhi Gajaria, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1