[gmx-users] rotate in editconf
T.A.Wassenaar
T.A.Wassenaar at rug.nl
Thu Jul 7 13:37:01 CEST 2005
Hi Attilio,
It's better not to rotate the box but to setup a new box
for the rotated system. Gromacs indeed only allows
triclinic boxes with the first vector aligned with the
x-axis, the second in the xy-plane and the third with a
positive z-component. But if you use editconf to setup a
box around the newly created system, then everything will
probably be fine.
Hope it helps,
Tsjerk
On Thu, 7 Jul 2005 13:09:59 +0200
Attilio Vargiu <vargiu at sissa.it> wrote:
> Hi Tsjerk,
> first, thanks for the answer!
> I already tried to generate a new box, rotating also the
>"box vectors" at the
> end of the gro file.
> But I read in the manual online that the gro format only
>supports cubic box in
> which the box vectors coincide with the axis, so I dont
>know how to do! In
> addition I tried to find something about g96 format,
>without success...
>
>
> Scrive "T.A.Wassenaar" <T.A.Wassenaar at rug.nl>:
>
>>
>> Hi Attilio,
>>
>> Do you construct a new box after rotation? editconf does
>> not change the box when rotating a system, and besides,
>> the box would probably be invalid anyway. So if you
>> haven't done so, try to generate a new box for the
>>rotated
>> system (translation doesn't matter).
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>>
>> On Wed, 06 Jul 2005 17:21:08 +0200
>> Attilio <vargiu at sissa.it> wrote:
>> > Hi all,
>> >
>> > I'm trying to implement umbrella sampling on my
>>system.
>> > My reaction coordinate is a distance between two atoms
>>A
>> >and B.
>> > Before starting the dynamics I rotated the system in
>> >order to align the vector AB with the z axis. To
>> >rototranslate the system I used editconf with the flag
>> >-rotate.
>> > In this manner I apply an harmonic constraint only in
>> >the z direction, allowing the system to explore phase
>> >space in the xy plane. This is my pull.ppa file:
>> >
>> > verbose = yes
>> > runtype=umbrella
>> > group_1=C_IMI
>> > reference_group=N_GUA
>> > reftype=com
>> > weights_1=
>> > pulldim=N N Y
>> > k1=15000;kJ/mol-1/nm-2
>> > pos1= 0 0 0.422
>> >
>> > But the dynamics died after 1-2 min, with this error:
>> >
>> > There are 24895 atoms in your xtc output selection
>> >
>> > t = 0.000 ps: Water molecule starting at atom 12323
>>can
>> >not be settled.
>> > Check for bad contacts and/or reduce the
>>timestep.Wrote
>> >pdb files with previous and current coordinates
>> > Large VCM(group IMI): -0.05608, -0.16218,
>> > -0.08893, ekin-cm: 5.55321e+00
>> > Group IMI with mass 2.97308e+02, Ekrot 6.00893e+00
>> >Det(I) = 1.31027e+02
>> > COM: 4.21794 4.56359 3.70009
>> > P: -16.67273 -48.21760 -26.44075
>> > V: -0.05608 -0.16218 -0.08893
>> > J: 11.75914 -12.46278 17.04114
>> > w: 0.39515 -0.24657 0.25223
>> > Inertia tensor (3x3):
>> > Inertia tensor[ 0]={ 3.36886e+01, -1.93692e+00,
>> >-1.95062e+01}
>> > Inertia tensor[ 1]={-1.93692e+00, 9.88940e-01,
>> > 2.37864e+00}
>> > Inertia tensor[ 2]={-1.95062e+01, 2.37864e+00,
>> > 1.75272e+01}
>> > Long Range LJ corr. to Epot: -891.161, Pres:
>> > -118.079, Vir: 5346.96
>> > Energies (kJ/mol)
>> > Bond G96Angle Proper Dih.
>> > LJ-14 Coulomb-14
>> > 8.73471e+02 1.88436e+03 2.22140e+03
>> > 8.62560e+02 -1.32192e+04
>> > LJ (SR) Disper. corr. Coulomb (SR) Coulomb
>> >(LR) Position Rest.
>> > 4.79055e+17 -8.91161e+02 -3.15962e+05
>> > -2.24687e+04 0.00000e+00
>> > Potential Kinetic En. Total Energy
>> > Temperature Pressure (bar)
>> > 4.79055e+17 nan nan
>> > nan nan
>> >
>> >
>> > t = 0.000 ps: Water molecule starting at atom 12446
>>can
>> >not be settled.
>> > Check for bad contacts and/or reduce the
>>timestep.Wrote
>> >pdb files with previous and current coordinates
>> >
>> > t = 0.000 ps: Water molecule starting at atom 12446
>>can
>> >not be settled.
>> > ..........
>> > ..........
>> > Check for bad contacts and/or reduce the
>>timestep.Wrote
>> >pdb files with previous and current coordinates
>> > Check for bad contacts and/or reduce the
>>timestep.Wrote
>> >pdb files with previous and current coordinates
>> >
>> > t = 0.001 ps: Water molecule starting at atom 12446
>>can
>> >not be settled.
>> > Check for bad contacts and/or reduce the
>>timestep.Wrote
>> >pdb files with previous and current coordinates
>> > Grid: -2147483648 x -2147483648 x -2147483648 cells
>> >Fatal error: ci = -1 should be in 0 .. -1 [FILE
>>nsgrid.c,
>> >LINE 218]
>> >
>> > Then I tried to run the original (without
>> >rototranslation) system, and this works without
>>problems
>> >(I tried both a normal dynamics and the one with the
>> >umbrella code).
>> > Incidentally I visualized with VMD both the system,
>>and
>> >it seems that periodic conditions are not well
>>conserved
>> >in the rototranslated system. In fact a simulation of
>> >this latter without periodic conditions proceed well.
>> >
>> > Does anybody kwow how to deal with this problem?
>> > Many thanks in advance,
>> >
>> > Attilio
>> >
>> > --
>> > Attilio Vittorio Vargiu
>> > PhD Student at SISSA/ISAS
>> > via Beirut 4
>> > I-34014 Trieste, Italy
>> > tel +390403787335 fax +390403787528
>> >
>> > _______________________________________________
>> > gmx-users mailing list
>> > gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please don't post (un)subscribe requests to the list.
>> >Use the www interface or send it to
>> >gmx-users-request at gromacs.org.
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list.
>>Use the
>> www interface or send it to
>>gmx-users-request at gromacs.org.
>>
>
>
>
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
> Powered by Horde http://www.horde.org/
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list.
>Use the
> www interface or send it to
>gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list