<span style="color: rgb(0, 0, 153);">Hello gmx-users,</span><br style="color: rgb(0, 0, 153);"><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">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.</span><br style="color: rgb(0, 0, 153);">
<span style="color: rgb(0, 0, 153);">However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message:</span><br style="color: rgb(0, 0, 153);"><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><span style="color: rgb(0, 0, 153);">I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful. </span><br style="color: rgb(0, 0, 153);">
<span style="color: rgb(0, 0, 153);">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?</span><br style="color: rgb(0, 0, 153);">
<span style="color: rgb(0, 0, 153);">Thank you in advance.</span><br><br>This is my grompp.mdp file configuration:<br>integrator = md <br>dt = 0.001 ; ps ! <br>nsteps = 1000000 ; <br>
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>