Hi Tsjerk, <br> Thanks for the hint. :-) I will check the compatability of isotropic scaling and parinello-rahman method. Thanks!<br><br>Liang<br><br><div><span class="gmail_quote">On 11/2/06, <b class="gmail_sendername">
Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Liang,<br><br>I'm not completely sure on this one, but isn't parinello-rahman per<br>definition anisotropic? Check the manual.<br>Regarding the second question, my usual answer is "there's no such<br>thing as a box in the infinite simulation system". There's only the
<br>lattice, which is defined by three vectors. But whether the shape of<br>the unit cell is allowed to change depends on the pressure coupling<br>you use. When using isotropic pressure coupling you're using a scalar<br>to scale the box vectors and your box shape (the angles between your
<br>vectors and the relative lengths) will be retained. But if I recall<br>correctly, parinello-rahman works by changing the box vectors based on<br>the "velocities" of these box vectors, which are scaled at every step
<br>to relax to the desired pressure. Thus, anisotropic pressure scaling.<br>You could try to use Berendsen pressure coupling.<br><br>Best,<br><br>Tsjerk<br><br><br>On 11/2/06, Liang Ma <<a href="mailto:liang.ma.1983@gmail.com">
liang.ma.1983@gmail.com</a>> wrote:<br>> Hi Tsjerk,<br>> Thanks for you fast reply. :-):-) Yes, I indeed used the isotropic<br>> pressure scaling method. That's why I found it's surpring that one<br>> dimension of my system actually shrinked. Is there any other possible reason
<br>> for this? Or, is there any constraint to keep the box shape always<br>> rhdo-like? If not, does gromacs always treat rhdo as triclinic and the box<br>> shaple actually is free to change?<br>><br>><br>
> Thanks a lot!<br>><br>> Liang<br>><br>> This is my grompp file:<br>><br>> ; title and include files<br>> title = salt<br>> cpp = cpp<br>> include =
<br>> -I/home/ma/gromacs/share/gromacs/top -I./<br>> define =<br>> ; integrator and input/output setting up<br>> integrator = md<br>> nsteps = 600000 ; 1.2 ns equilibration
<br>> dt = 0.002<br>> nstxout = 5000<br>> nstvout = 5000<br>> nstenergy = 500<br>> nstxtcout = 500<br>> nstlog = 500
<br>> xtc_grps = System<br>> energygrps = System<br>> comm_mode = none<br>> ; neighbor searching and vdw/pme setting up<br>> nstlist = 10<br>> ns_type = grid
<br>> pbc = xyz<br>> rlist = 1.4<br>><br>> coulombtype = pme<br>> fourierspacing = 0.1<br>> pme_order = 6<br>> rcoulomb =
1.4<br>><br>> vdwtype = switch<br>> rvdw_switch = 1.0<br>> rvdw = 1.2<br>><br>> ; cpt control<br>> tcoupl = nose-hoover<br>> tc-grps = System
<br>> tau_t = 0.1<br>> ref_t = 300<br>> Pcoupl = parrinello-rahman<br>> pcoupltype = isotropic<br>> tau_p = 1.0<br>> compressibility =
4.5e-5<br>> ref_p = 1.0<br>><br>> ; velocity & temperature control<br>> gen_vel = no<br>> gen_temp = 300<br>> annealing = no<br>> constraints = hbonds
<br>> constraint_algorithm = shake<br>> morse = no<br>><br>><br>><br>><br>> On 11/2/06, Tsjerk Wassenaar < <a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:
<br>> ><br>> > Hi Liang,<br>> ><br>> > Apparently, your system contracted in one direction. You can avoid<br>> > this by simulating at constant volume or by using isotropic pressure<br>> > coupling.
<br>> > Your protein should not have direct interactions with its periodic<br>> > images during the simulation. This usually means you can discard your<br>> > results.<br>> > The last two values are the x and y skewing of the third vector
<br>> > defining your periodic lattice (the periodic boundary conditions).<br>> > Likewise, the first two zeros are the y and z skewing of the first<br>> > vector and the other two zeros are the x and z skewing of the second
<br>> > vector. You can check chapter 3 of the gromacs manual to get to know<br>> > more about periodic boundary conditions in gromacs.<br>> ><br>> > Best,<br>> ><br>> > Tsjerk<br>> >
<br>> > On 11/2/06, Liang Ma <<a href="mailto:liang.ma.1983@gmail.com">liang.ma.1983@gmail.com</a>> wrote:<br>> > > Hi all gromacs users,<br>> > > I am simulating a protein in explicit solvent with Periodic
<br>> boundary<br>> > > condition and PME . The box type I used<br>> > > is rhdo (rhombic dodecahedron). However, I checked the box length and<br>> angle<br>> > > during simulations, it deviates far away from the normal rhdo box
<br>> shape.<br>> > > For example, the third line in pdb at the beginning is :<br>> > > CRYST1 90.093 90.093 90.093 60.00 60.00 90.00 P 1 1<br>> > > which is a perfect rhdo box.
<br>> > ><br>> > > During the simulation, it changed to:<br>> > > CRYST1 89.503 89.503 68.425 105.59 105.59 90.00 P 1 1<br>> > > ,which is not rhdo.<br>> > > Meanwhile, the distance between the protein and its nearst image
<br>> decreased<br>> > > dramatically, (they even touched).<br>> > > So my question is this normal? If not, is there any way to constraint<br>> the<br>> > > box always in a rhdo box shape (a=b=c)
<br>> > ><br>> > > And also,<br>> > > the last line in the gro file changed to:<br>> > > 8.95030 8.95030 6.32914 0.00000 0.00000 0.00000 0.00000<br>> > > -1.83879 -
1.83879<br>> > > what does the last two negative values exactly mean?<br>> > ><br>> > ><br>> > > Thanks for any help!<br>> > > Liang<br>> > ><br>> > > _______________________________________________
<br>> > > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
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Ph.D.<br>> > post-doc<br>> > NMR, Utrecht University,<br>> > Padualaan 8,<br>> > 3584 CH Utrecht, the Netherlands<br>> > P: +31-30-2539931<br>> > F: +31-30-2537623<br>> > _______________________________________________
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</a><br>><br>><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>post-doc<br>NMR, Utrecht University,<br>Padualaan 8,<br>3584 CH Utrecht, the Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>_______________________________________________
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