[gmx-users] gmx sasa

Hello Gromacs Users, "gmx sasa" in Gromacs 5.0.6 returns a message stating that all atom radii are obtained from the following reference: "A. Bondi, van der Waals Volumes and Radii, J. Phys. Chem. 68 (1964) pp. 441-451" Can the user still control the radii used by editing a local copy of the

Re: [gmx-users] gmx sasa

On 1/31/16 2:24 PM, Eric Smoll wrote: Hello Gromacs Users, "gmx sasa" in Gromacs 5.0.6 returns a message stating that all atom radii are obtained from the following reference: "A. Bondi, van der Waals Volumes and Radii, J. Phys. Chem. 68 (1964) pp. 441-451" Can the user still control the

[gmx-users] weird configuration when pulling rate is small

Dear list, I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow far away), but the simulations run well and the

Re: [gmx-users] weird configuration when pulling rate is small

Hi Ming Tang, Might that be due to PBC? Try gmx trjconv -pbc nojump Cheers, Tsjerk Dear list, I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 1

how to run gromacs for protein protein interaction having phosphorylated at SER and THR. error: residue TPO not found in residue topology database modification are done from the given web. http://www.gromacs.org/Downloads/User_contributions/Force_fields >make changes in .rtp file make changes in

Re: [gmx-users] gmx bundle

Hi, That means the calculation failed somehow (e.g. you asked for a dihedral angle between four co-linear atoms, or divided by zero, or something like that) but we don't have any clues on why (at this stage). Mark On Mon, Feb 1, 2016 at 6:22 AM Felix W.-H. Weng wrote: >

Re: [gmx-users] gromacs error

how to run gromacs for protein protein interaction having phosphorylated at SER and THR. error: residue TPO not found in residue topology database modification are done from the given web. http://www.gromacs.org/Downloads/User_contributions/Force_fields >make changes in .rtp file make changes in

[gmx-users] Low GPU utilization

Dear Gromacs users, I'm running a simulation between LASR receptor and Quercetin on Q6600, GTX 960, CPU utilization is about 90%, but GPU is only 25-30%(Nvidia X server tools).The system is only 28643 atoms and dt = 2 fs. This is the mdp settings: ; Run parametersdefine      = -DPOSRES_B ; Lets

[gmx-users] gmx bundle

Dear all: I'm trying to calculate kinks within alpha helices using gmx bundle. I specify 4 Ca atoms from the helix top, bottom and kink separately in the index file. And, I've used the option -na 1. But I keep getting the results shown below. @title "Kink angles" @xaxis label "Time

Re: [gmx-users] g_count

Hi, g_count has never been a part of GROMACS. You can find it elsewhere though, via a Google search. Mark On Mon, Feb 1, 2016 at 5:00 AM vgsplayer1 wrote: > > > hello all > I want to cuout the numbers of molecules within a cylindrical region as a > function of time. >

[gmx-users] g_count

hello all I want to cuout the numbers of molecules within a cylindrical region as a function of time. However, i can not found the g_count in GMX 4.6.7？ Which command could replace it in 4.6.7? -- Yipeng Cao Ph.D. Institute of Physics, Nankai University Tianjin China -- Gromacs Users

[gmx-users] relative binding free energy calculation Gromacs 5.0.5

Dear users, I’m performing relative binding free energy calculation in Gromacs 5.0.5. In the mdp files I’m using the following section free-energy = yes init_lambda_state= LAMBDA fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

Re: [gmx-users] relative binding free energy calculation Gromacs 5.0.5

What do you mean by "instability"? You also don't quite say what these values mean but I guess they are the estimates of the free energy per each window as computed by different methods(?). These values come obviously from the (linear) electrostatic transformation so playing with softcore