<br><br><div class="gmail_quote">On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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"><br>
<br>
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>
<br>
I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful.<br>
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>
</blockquote>
<br></div>
It seems to me that your system is simply too small to perform this kind of operation. By applying 1000 bar of pressure to such a small system, you can certainly expect the box size to deform and get smaller. Perhaps a larger number of molecules (and thus a larger box) will give you a reasonably-sized box once the 1000 bar of pressure has been applied and the system equilibrated.<br>
</blockquote><div><span style="color: rgb(0, 0, 153);"><br>Yes I think I should increase my simulation size as pointed out by Mark. </span><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also note that haphazardly changing the vdwtype or rvdw can have negative impacts on your simulation, depending on your chosen force field's sensitivity to these parameters.<br></blockquote><div><span style="color: rgb(0, 0, 153);"><br>
Thank you for pointing this out. I am relatively new to this method so am taking "figure out as I go" approach.</span><br><br style="color: rgb(0, 0, 153);"><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-Justin<br>
<br>
<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">
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>
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</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
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</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>