Re: [gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

Hi Peter, Thanks for the reply. I'm not using the contact information at all (-on is unspecified), and yes, it still generates a result for >6A in the distance output (-od) , but the result for which atoms are at the reported distance is sometimes missing from the atom pair output (-o) file. MZ

Re: [gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

I have not read the source, but the default search radius for mindist is 6A. If you have no contacts within 6A of the atoms in the primary group to the target group for a given frame, will it still generate a result, since for all intents and purposes the array search should be null in that case?

[gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

Hi all, I'm running g_mindist (from 4.5.5) on a slew of very short trajectories (51 frames) in order to obtain both minimum distances and the corresponding atom pairs, using echo 10 11 | g_mindist -nice 10 -f seg.xtc -n $NDX -s $TPR -nopbc -o mindist_pairs.out -xvg none where NDX and TPR are (va

Re: [gmx-users] g_mindist -on

On 9/11/2011 9:09 PM, Steven Neumann wrote: Dear gmx Users, I am wondering what is the value of Number of Contacts (<0.6 nm) between two groups. When I specify one group - Ligand and second - protein residue - does it count every dostance within 0.6 nm between every atom from one group and eve

[gmx-users] g_mindist -on

Dear gmx Users, I am wondering what is the value of Number of Contacts (<0.6 nm) between two groups. When I specify one group - Ligand and second - protein residue - does it count every dostance within 0.6 nm between every atom from one group and every atom from the second specified group? Cheers

[gmx-users] g_mindist on rhombic dodecahedron system

Dear users, following Tsjerk' suggestions, I simulate the protein which had some problems in periodic distance violations in a triclinic box, using instead a rhombic dodecahedron box created with the options: editconf -f prot.gro -o prot_boxdod.gro -bt dodecahedron -d 1.5 -c Minimization, PR-NV