[gmx-users] PMF using umbrella sampling

Hello everyone, I'm trying to compute the PMF for pulling two proteins apart. I'm planning on setting up several runs where the COM separation of the proteins is constrained and the constraint force is measured over the course of a long simulation. However, I'm having trouble doing this because I'm

Re: [gmx-users] PMF using umbrella sampling

you do with the new Windows Live? Find out > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please

[gmx-users] gb_saltconc in implicit water simulations

clude explicit counterions to neutralize the system when using implicit solvent. Is there a typical protocol one follows to neutralize charged systems when using implicit solvent? Thanks, Bob -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th S

[gmx-users] Re: gb_saltconc in implicit water simulations

Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson wrote: > Hello everyone, > I am trying to use implicit solvent with a CG DNA model. The model, > however, uses explicit charges, which means tha

[gmx-users] Columns in log file of g_cluster

Hello everyone, What do columns 3 and 5 (the rmsd numbers next to the number of structures in the cluster and the frame number of the central cluster, respectively) indicate in the log file of g_cluster? Thanks, Bob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

[gmx-users] Negative number of RMSD calculations left in g_cluster

ion skip 2 (35000 frames instead of 69000) and it works fine. What is the reason for the negative number of RMSD calculations and how can it be fixed? Thanks, Bob -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA

[gmx-users] Energy Group Exclusions

kind of energy group exclusions whatsoever? It's obvious to me that if my substrate were charged it would also contribute to the PME calculation. Thus, the Coulomb energy of the substrate would be impossible to get rid of. Is my thinking correct? Thanks, B

[gmx-users] g_dipoles -slab option

.500 -0.103 0.057 -0.023 0.119 7.500 0.000 0.000 0.000 0.000 8.500 0.000 0.000 0.000 0.000 9.500 0.000 0.000 0.000 0.000 Thanks, Bob Johnson ___ gmx

[gmx-users] AFM Pulling Rate

N N Y afm_rate1 = 0.05 afm_k1 = 100 afm_dir1 = 0 0 1 I'm using version 3.3. Does anyone know what's going on? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don'

[gmx-users] Generating a PQR file

ay to extract this information from a .tpr file? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or

[gmx-users] Measuring dihedral energy of various selections

Hello everyone, I would like to measure the dihedral energy of certain portions of the same molecule over the course of a previously calculated trajectory. It's important that I get the energy of ONLY these portions. I thought of saving the trajectory of the portion in interest using trjconv. Then

[gmx-users] File input/output error: Can not determine precision of trn file

Hello everyone, It seems that one of my trajectory files has an error. I get the following message when using trjconv -f trajectory.trr. File input/output error: Can not determine precision of trn file I noticed that there was a previous question about this error message. However, the only availa

[gmx-users] Calculation of Electrostatic Potential at a Nanotube

Hello everyone, I am trying to calculate the electrostatic potential at the surface of a carbon nanotube from an MD simulation involving water and other adsorbates binding to the nanotube. Since the nanotube atoms are uncharged this is how I was proceeding: 1. I computed the trajectory using the n

[gmx-users] x2top stalls when generating topology file

Hello everyone, There has been other reports on the mailing list where users attempt to generate a topology with x2top only to have the program stall and generate no output. I'm using x2top (from Gromacs version 3.3.1) to generate topology files for infinite carbon nanotubes and graphene sheets. St

[gmx-users] Launching Replica Exchange MD

Hello everyone, I can't seem to find how to start a replica exchange MD job. I have a separate .tpr file for each replica. How do I give these to mdrun? Also, for debugging purposes I wanted to run a few of my replicas on the same node (otherwise I have to wait in a queue) just to make sure my acce

[gmx-users] Dummy atoms for electrostatics calculation

do not want the nanotube charges to affect the dynamics of the molecules in the environment. In other words, I want the DNA, water, counterions to see an uncharged nanotube for the purpose of calculating the trajectories. Is there any way to do this with dummy atoms? Thanks, Bob Johnson

[gmx-users] Restarting a periodic simulated annealing run

400K and proceeds in the same direction as when it ended? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www in

[gmx-users] Non-zero system charge

Hello everyone, I am using PME to handle electrostatics. What happens if I run a simulation with a non-zero net charge? Does GROMACS automatically provide some sort of background charge to neutralize the system? Thanks, Bob Johnson ___ gmx-users mailing

[gmx-users] Orientation restraints

x27;t think using angle restraints is sufficient for what I want to do because there you can only restrain pairs of atoms. Any ideas how I could define a normal vector to each plane and have that maintain a 90 degree angle with respect to the z-axis? Thanks, Bob Jo

[gmx-users] Radial distance restraints

z-axis or change their orientation with respect to the nanotube surface. That is why only radial constraints (sqrt(x^2 + y^2) = constant) will work. Any way to do this? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.g

[gmx-users] Implementing Radial Distance Constraints

. Here R0 is the fixed radial distance. Is this difficult to implement in Gromacs? What file in the source code would I edit? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Re: Implementing Radial Distance Constraints

>please be more clear. > >if we assume your cnt is centered along the z-axis, given roughly by >x^2+y^2 = d0. Am I correct in assuming that you want all other particles >to have x^2+y^2 <= d1, where d1 < d0 ? > >-- >David. The molecules in my system adsorb to the tube's outer wall. They are not in

[gmx-users] Huge fluctuations for pressure coupling

Hello everyone, I have a 20 base single stranded DNA with counterions that is hydrated with about 9000 water molecules. My pressure coupling input looks like this: pcoupl = Parrinello-Rahman pcoupltype = isotropic ref_p = 1.01 compressibility = 4.5e-5 ta

[gmx-users] Simulating a substrate

at LJ parameters I should use for the substrate. Any ideas? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www in