I'm getting odd behavior with the reference configuration generated by g_sdf (v. 3.3.3). I am wondering if this is a bug, and if the spatial density profile is similarly affected.
My test system has simple, regular geometry: a glycine 15-mer held frozen in a fully extended "rod-like" configuration, with water solvent. I wish to evaluate, for instance, the spatial distribution of water O around the 15 instances of the glycine O. My understanding is that g_sdf will average the water oxygen SDF around the 15 sites to yield one composite SDF -- is this correct? However, the reference configuration, given by g_sdf -r, seems incorrect when performing the SDF around more than one atom triplet. Based on the documentation, Atom 1 (the GLY O) should be at the origin, and Atom 2 (GLY C) should be offset along the Z-axis only. When there is only one atom triplet (that is, performing sdf around just one GLY O), this is in fact the case. However, when performing an SDF around more than one atom, this is no longer holds, and the offset increases with increasing number of triplets. Below I give the output of three reference .gro files illustrating this. In all cases, Atom 1 is GLY O, Atom 2 is GLY C, Atom 3 is GLY CA; Atom 4 is Water OW. My question is, first, should I expect the GLY O to lie at the origin in all instances? Is this a bug, or user error? And if this is a bug, are the sdf data reliable? Regards, Matt --- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering Pappu Lab: http://lima.wustl.edu Washington University in St. Louis Reference Configuration .gro files: (constructed with, e.g. g_sdf -f ../traj.xtc -n index-all.ndx -s ../GLY15Frozen.tpr -o OO-all -r OO-all -grid 2 2 2 -b 500 ) For one GLY residue: Protein 7 4 GLY N 1 0.187 0.033 -0.090 4 GLY H 2 0.041 0.046 -0.090 4 GLY CA 3 -0.000 0.193 -0.089 4 GLY HA1 4 0.086 0.281 -0.088 4 GLY HA2 5 0.243 0.119 -0.091 4 GLY C 6 -0.000 0.000 -0.179 ; OFFSET ALONG Z AXIS 4 GLY O 7 0.000 0.000 0.000 ; AT ORIGIN 10.00000 10.00000 10.00000 For two GLY residues: Protein 7 4 GLY N 1 0.575 -0.257 -0.087 4 GLY H 2 0.430 -0.244 -0.086 4 GLY CA 3 0.389 -0.097 -0.088 4 GLY HA1 4 0.474 -0.009 -0.089 4 GLY HA2 5 0.632 -0.171 -0.090 4 GLY C 6 0.388 -0.291 -0.175 4 GLY O 7 0.389 -0.288 0.005 ; NOT AT ORIGIN 10.00000 10.00000 10.00000 For all 15 GLY residues: Protein 7 2 GLY N 1 -1.438 1.227 -0.102 2 GLY H 2 -1.551 1.280 -0.097 2 GLY CA 3 -1.631 1.377 -0.104 2 GLY HA1 4 -1.595 1.400 -0.112 2 GLY HA2 5 -1.421 1.256 -0.109 2 GLY C 6 -1.572 1.263 -0.123 2 GLY O 7 -1.564 1.272 -0.064 ; NOT AT ORIGIN 10.00000 10.00000 10.00000 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php