<br><br><div class="gmail_quote">On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Yongchul Chung wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello gmx-users,<br>
<br>
I am running an NPT simulation with 100 molecules of n-alkane and trying to impose uni-axial pressure of these molecules using semiisotropic option in grompp.mdp.<br>
However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message:<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.0.5<br>
Source code file: ns.c, line: 2295<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br>
-------------------------------------------------------<br>
</blockquote>
<br></div>
You're imposing 1000 bar of pressure along the z-axis. Surely you should expect distortion?<br>
<br>
You should do some maths and work out the expected density of the box under such pressure. You still need a box large enough that the maximum cut-off length can be satisfied, so that sets the minimum number of molecules you need, and thus the initial size of the box.<div class="im">
<br></div></blockquote><div><br>Thanks for the input. I should do this.<br><br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful.<br>
</blockquote>
<br></div>
Don't fool with .mdp settings hoping it'll magically work. Read how they work, and you might have understood why the minimum image convention requires that the condition that provoked the above error does not arise.<br>
<font color="#888888">
<br>
Mark</font><br></blockquote><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><font color="#888888">
</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
is there any other options in gromacs that I can use to impose uniaxial stress? Or does anyone had any similar problems related to semi-isotropic pressure coupling?<br>
Thank you in advance.<br>
<br>
This is my grompp.mdp file configuration:<br>
integrator = md<br>
dt = 0.001 ; ps !<br>
nsteps = 1000000 ; nstcomm = 1<br>
nstxout = 250 ; collect data every 0.5 ps<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 10<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 0.9<br>
<br>
coulombtype = PME<br>
rcoulomb = 0.9<br>
vdwtype = switch<br>
rvdw = 0.7<br>
rvdw_switch = 0.0<br>
<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
; temperature coupling is on<br>
Tcoupl = v-rescale<br>
; Groups to couple separately<br>
tc-grps = System<br>
; Time constant (ps) and reference temperature (K)<br>
tau_t = 0.1<br>
ref_t = 300<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
constraints = all-bonds<br>
<br>
; pressure coupling is on<br>
pcoupl = parrinello-rahman<br>
pcoupltype = semiisotropic<br>
<br>
tau_p = 0.5<br>
compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction<br>
ref_p = 1.0 1000.0 ;x/y-direction, z-direction<br>
<br>
<br>
<br>
-- <br>
Yongchul "Greg" Chung<br>
Graduate Student<br>
Dept. of Chemical Engineering, Case Western Reserve University<br>
<br>
<br></div></div>
------------------------------------------------------------------------<div class="im"><br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></blockquote><div><div></div><div class="h5">
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yongchul "Greg" Chung<br>Graduate Student<br>Dept. of Chemical Engineering, Case Western Reserve University<br>