Hi Michael, if you are not interested in the substrate dynamics, then you could try the freeze group options (freezegrps and freezedim). I have used these options for graphite and it worked just fine. best, André
> Dear Listmembers, > > This post is quite lengthy because it contains several different problems > that > I came across during my simulations and that I cannot figure out up to > now. I > included some links to pictures to give you some visualization and would > be > glad for every suggestion or hint even to part of my problems. > > Generally for my simulations I need substrates of silicon oxide and > graphite > (each one in different simulations). The substrate fills the simulation > box > completely in x-y direction so it should look like an infinite surface > considering the periodic boundary conditions. > > The simulation with silicon oxide is working fine but I experienced some > strange thing though: When the .gro file contains negative coordinates and > I > generate a .tpr for 4 nodes the structure is messed up totally after > energy > minimization (although it converges and gives no errors). I guess that the > breaking up in four parts is somehow connected to the 4 nodes, because > generating and running a 1 node .tpr solves this problem and the structure > keeps intact after em - see pictures here: ( http://tinyurl.com/59zfda ). > When > I shift the coordinates in the .gro with editconf so that every coordinate > is > positive the structure can be em with both 1 or 4 node without problems. > > For the main md I have to stick with 1 node anyway because I get a "Shake > block crossing node boundaries" error when I try to use 4 nodes. I found > the > advise to use less nodes in the mailing list archives and as I said it > works > for me, too, but is there any other way to get around this? For the test > runs > I'm doing now 1 node is fine, but for the real simulations later on I > would > like to use more nodes because the system will get bigger... > > With the graphite I have another problem: Again I have to stick with only > one > node, otherwise the structure is broken after energy minimization (with 4 > nodes http://tinyurl.com/5eqngz ). Additionally here the energy > minimization > is not converging even after 2500 steps, forces keep in the range of 10^4 > but > I can still do a md with this file that is not exploding (md with the > starting > structure without any energy minimization will result in an exploding > system > as one might expect). After energy minimization the graphite sheets (four > are > in the simulation) are bended up/down correspondently to the connected > periodic boundary at the edges of the simulation box (box is triclinic, > http://tinyurl.com/5m72ke ). When I run an md with this as starting > structure > without position restraints on the carbon atoms, the sheets cleave > beginning > from the edges and then reunite in a curled conformation within 10ps ( > http://tinyurl.com/5j4l3z ). > > If I put position restraints on all carbon atoms the graphite keeps flat, > but > of course I still have the up/down bending at the box edges, which I also > want > to get rid off to have a real "infinite" graphite surface. > > First I thought that this was maybe a problem of my graphite structure not > fitting into my simulation box (hence the curling of the surface) but I > checked the bonding lengths and b0 in the topology, the unit cell vectors > and > box vectors thoroughly and everything seems to be right. If I copy my > simulation box and shift it by one of the box vectors I get a perfect > continuation without any deviation on the boundaries, so everything seems > like > it should be for the starting structure. > > I also simulated the same graphite sheets within a bigger box, so that > border > carbons could not feel their counterparts over the periodic boundaries. > That > gave no distortion at the edges after em and the em converged, but of > course > in this way I cannot get an continous surface. > > Even stranger is, that after em the whole structure coordinates are > shifted > into the neighbouring periodic cell! For a bigger system with some > additionally molecules that should absorb to the graphite surface the > graphite > sheets even ended up in different periodic images of the simulation box > after > em ( http://tinyurl.com/5uaxfa ). Maybe that's more a visualization > problem > because the following md simulation shows, that the molecules adsorb to > the > surface nevertheless (as one would suggest from pbc). Of course I can > reconfigure my .gro for visualization by substracting or adding the box > vectors untill all atoms end up inside the 'real' simulation box, but is > it > really supposed to behave that way, or is there something definitely wrong > with my structure? > > I saw this "shifting" of the whole substrate into another periodic image > of > the simulation box also in the simulation with the silicon substrate: it > 'jumped' into the periodic cell and then jumped back one frame later. > The other present (small) molecules stayed in the real simulation box all > the > time. I guess that this is maybe a problem caused by the substrate > "molecule" > filling up the whole simulation cell (at least in xy), but is there a way > of > getting Gromacs to always write out coordinates that lie within the real > simulation cell instead of an periodic image? > > And is there a way of defining bonds over the periodic boundaries? When I > tried this it always seemed as if Gromacs interpreted these bonds as > extremly > overstretched bonds (that are stretched over the whole simulation box > instead of just reaching the "short way" over the periodic boundary) > yielding > crippled structures ( http://tinyurl.com/54uvs4 ). > > All simulations used the ffG43b1 force field. Cutoffs of 1.2 and an Rlist > of > 1.4. Coulomb was shifted from 0.0 and VdW from 0.9. Timestep was 2 fs and > pbc > = xyz. The boxes were large in z direction to generate xy pbc. I can also > put > the topologies online if someone would like to look at them. > > I hope anyone can give me some advice because although I tried a lot of > things > right now I feel not like coming close to a solution for my problems. :( > > Best regards, > Michael > -- > http://www.defux.de > _______________________________________________ > 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 > &*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*& Prof. Dr. André Farias de Moura Departamento de Química Universidade Federal de São Carlos São Carlos - SP - Brasil tel. 16-3351-8090 &*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*& _______________________________________________ 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
