Re: [gmx-users] minimum distance between the protein and its mirror image

The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set? > 在 2016年8月29日，下午8:58，Justin Lemkul 写道： > > > > On 8/29/16 5:02 AM, YanhuaOuyang wrote: >> Hi, >> I am running a REMD of

[gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

Dear Gromacs Users, I have a Fatal error as follow. The error says -rdd option or -ddcheck. How can I properly use these options? Is the following command the proper use of these options? > gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5 -ddcheck Thank you. 1 of the

Re: [gmx-users] Grace on Mac OS

You might try homebrew: http://brewformulas.org/Grace. Daryl C. Chrzan Professor, Materials Science and Engineering Vice Chair for Academic Affairs, Materials Science and Engineering Chair, Applied Science and Technology University of California Berkeley, CA

[gmx-users] Grace on Mac OS

Hi, I am trying to see .xvg plots in Mac OS 10.11.3, so that I can avoid ubuntu and save some time if possible. I follow this link: http://www.phy.ohiou.edu/~hadizade/MRHadizadeh/Blog/Entries/2013/8/5_Installing_XmGrace_(Grace)_on_Mac_OS_X.html but during the installation of

Re: [gmx-users] Fwd: tau-t effects on sd integrator

Thank you very much, Justin. I'll go and try with 2ps. Best wishes, Sidong On Mon, Aug 29, 2016 at 1:38 PM, Justin Lemkul wrote: > > > On 8/29/16 1:29 PM, Sidong Tu wrote: > >> Dear all, >> >> I was trying to simulate lysozyme and polymer in water model tip3p using >>

Re: [gmx-users] QM/MM simulations

Hi, Sadly, most of the QM/MM interfaces have been lacking a maintainer on the GROMACS side for quite a number of years. You should definitely be following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely. Mark On Mon, Aug 29, 2016 at 9:36 PM Clinton King wrote: >

[gmx-users] QM/MM simulations

I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation of a single molecule of octanol in a box of water. In examining the standard output, it appears that call to Gaussian is proceeding as expected, but looking at the log file, it doesn't appear that quantum energy is being

[gmx-users] evaluation of influence of pH on the stability of protein

Hi all Gmx usersI want to evaluate influence of pH on the stability of  protein.  can I use MD simulation for this goal? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Fwd: tau-t effects on sd integrator

On 8/29/16 1:29 PM, Sidong Tu wrote: Dear all, I was trying to simulate lysozyme and polymer in water model tip3p using charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and the system size was about 60,000 atoms. I used sd as integrator and the tau-t option was 0.1. I

[gmx-users] Fwd: tau-t effects on sd integrator

Dear all, I was trying to simulate lysozyme and polymer in water model tip3p using charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and the system size was about 60,000 atoms. I used sd as integrator and the tau-t option was 0.1. I wondered if there is any problem with this

[gmx-users] calculation of pKa

Dear Gromacs users, I am trying to perform a pKa calculation of a Cys in a thioredoxin-protein (Trx) using the FEP implementation of Gromacs 5.1.0. I am transforming the charge in CYS to that of a CYM in 10 equally-spaced lambda steps, and then turning off the vdw radii of the hydrogen (HS) in

Re: [gmx-users] Segmentation fault

Please make sure to use a proper subject line and do not reply to the entire digest. On 8/29/16 6:16 AM, Seera Suryanarayana wrote: Sub: Segmentation fault Dear Justin and Vivek, I came to know what was my fault. I added the refcoordscale = com in .mdp file and it going fine. I have

Re: [gmx-users] minimum distance between the protein and its mirror image

On 8/29/16 5:02 AM, YanhuaOuyang wrote: Hi, I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge. Then I use "gmx mindist " to check if a protein has seen its periodic image during simulation. When

Re: [gmx-users] Mass Weighted Covariance matrix

On 8/29/16 12:16 AM, Tushar Modi wrote: Hello I am trying to calculate mass weighted covariance matrix using a Gromacs Topology file and a trajectory file . The trajectory has only protein coordinates. I am using "gmx_mpi covar" function for the same. I am using following format from the

Re: [gmx-users] KALP-15 tutorial

On 8/28/16 11:13 AM, Roshan Shrestha wrote: Actually, I thought that I made an error by minimizing system.gro instead of system_inflated.gro. So, I ran energy minimization for system_inflated.gro by renaming tutorial's minim.mdp as em.mdp- gmx grompp -f em.mdp -c system_inflated.gro -p

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 102

Sub: Segmentation fault Dear Justin and Vivek, I came to know what was my fault. I added the refcoordscale = com in .mdp file and it going fine. I have through the many references for refcoordscale, despite of some information I am not getting what exactly it is? Kindly give me some hit.

Re: [gmx-users] Finding Average Net charge as a function of distance from a polymer segment

Dear Gromacs Users I want to examine the distribution of counterions in my system at larger length scales comparable to the size of the molecule. I have used RDF's to find the distribution of ions till half the box size. Can I consider half the box size as larger length scale ? I have found in a

[gmx-users] minimum distance between the protein and its mirror image

Hi, I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge. Then I use "gmx mindist " to check if a protein has seen its periodic image during simulation. When I used the command "gmx mindist -f