Hi, I am running NVE simulations of a system of 1000 water molecules. I am attempting to run analogous simulations on Gromacs 4.5.4 and also on another MD program. Once finished, I will compare the results of the two programs. It was suggested to me that to compare the results of the two programs in a step-by-step manner, as a first step I should run the simulations with the electrostatics (both short-range and long-range interactions) turned off. In other words, run the simulations considering only Lennard-Jones interactions. My question is, what is the best way to do this in Gromacs?
A (very much more experienced) colleague suggested that I "turn off electrostatics" by simply setting all the charges to zero. However, when I look into the topology and structure files, I see some surprising (to me) things -- the charges do not appear to be specified in the .top and .gro files. To back up, I will first try to explain my system. I have a PDB file specifying 1000 water molecules that someone gave me. This PDB file looks like the following: TITLE water REMARK THIS IS A SIMULATION BOX CRYST1 47.100 47.100 47.100 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 OW SOL 1 -21.177 -21.195 -21.179 1.00 0.00 ATOM 2 HW1 SOL 1 -21.671 -21.195 -22.083 1.00 0.00 ATOM 3 HW2 SOL 1 -21.863 -21.195 -20.412 1.00 0.00 ATOM 4 OW SOL 2 -16.467 -21.195 -21.179 1.00 0.00 ATOM 5 HW1 SOL 2 -16.961 -21.195 -22.083 1.00 0.00 ATOM 6 HW2 SOL 2 -17.153 -21.195 -20.412 1.00 0.00 ... And so on. According to the PDB file format specification (http://www.wwpdb.org/format/sect9.html), the last two columns in my file correspond to the occupancies and temperature factors, respectively, of my atom. So, evidently, partial charges on the oxygen and hydrogens are not specified in this PDB file. Next, I execute the command: pdb2gmx -f water.pdb -p water.top -i water.itp -o water_processed.gro And, when prompted, I choose the OPLS-AA force field and the SPC/E water model. Apparently, Gromacs recognizes from my PDB file that my system contains water (and only water). Alternatively, I could have created a topology file manually, without pdb2gmx, by simply creating a .top file containing: ------ #include "oplsaa.ff/forcefield.itp" #include "oplsaa.ff/spce.itp" [ system ] water [ molecules ] SOL 1000 ------ and then simply feed grompp the topology file and the original PDB file when preparing for a dynamics run (pdb2gmx, I understand, is meant for chains rather than multiple molecules). But, in any case, I took the long road and used pdb2gmx to create the .top topology and a .gro coordinate file. What surprises me (a novice in Gromacs and MD in general), though, is that it seems that neither the .top file nor the .gro file contains any reference to the charges on the oxygens and hydrogens in this water-only system. For example, my .top file contains: ------ ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" ; Include water topology #include "oplsaa.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "oplsaa.ff/ions.itp" [ system ] ; Name water [ molecules ] ; Compound #mols SOL 1000 ------ And, my .gro file contains, for example: ------ water 3000 1HOH OW 1 -2.118 -2.119 -2.118 1HOH HW1 2 -2.167 -2.119 -2.208 1HOH HW2 3 -2.186 -2.119 -2.041 2HOH OW 4 -1.647 -2.119 -2.118 2HOH HW1 5 -1.696 -2.119 -2.208 2HOH HW2 6 -1.715 -2.119 -2.041 ... 4.71000 4.71000 4.71000 ------ So, as far as I can tell, neither my .top nor my .gro file specify the charges on the atoms. I guess that this means that the charges on the atoms are only specified in the spce.itp file. When I find and open the spce.itp file, I see: ------ [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_116 1 SOL OW 1 -0.8476 2 opls_117 1 SOL HW1 1 0.4238 3 opls_117 1 SOL HW2 1 0.4238 #ifndef FLEXIBLE [ settles ] ; OW funct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #endif ------ So, there the charges are specified: -0.8476 on the oxygen and 0.4238 on each hydrogen. Coming back to my original goal--to "turn off electrostatics" by zeroing the charges--I could in principle just set the charges in this .itp file to 0. However, on our cluster, this file appears to be READ ONLY. So to change the charges to 0, I need to see if I can get permission from our administrator. Based on my story above, my questions are: 1. Is there a better way to "turn off electrostatics"--without modifying the spce.itp file? 2. Why does it seem that charges are not specified in the .top and .gro files? Is this just because I am boringly simulating only a solvent, and the topology file tells Gromacs to look in spce.itp when simulating the water molecules? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
