<div class="gmail_quote"><font face="tahoma,sans-serif">Hi all,</font><div><font face="tahoma,sans-serif"><br></font></div><div><font face="tahoma,sans-serif">I'm currently trying to run a simple test on how electrostatics are handled in gromacs when the slab Ewald summation is used. My system consists of 26 point charges, with 25 arranged in a square lattice in the XY plane and the 26th above the charge in the middle. My goal is to calculate the force on the particle above and the total electrostatic energy. I have written my own coordinate and topology files, and they grompp just fine, but when I try to mdrun for just one step, I get a segfault. Trajectory files are still produced, but when I try to have trjconv output the forces, it just writes the coordinates. The command I used was:</font></div>
<div><font face="tahoma,sans-serif"><div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="color:rgb(0, 0, 0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">trjconv -f traj.trr -s topol.tpr -n index.ndx -novel -force -o results.gro</span></div>
<div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="color:rgb(0, 0, 0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">I've set nxtxout, nxtvout and nxtfout to 1 in my mdp file, so if not for the segfault, I believe I should have force data. How can I fix the segfault?</span></div>
<div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="color:rgb(0, 0, 0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><br>
</span></div><div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="white-space:pre-wrap">.itp file for charges:</span></div>
<div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="white-space:pre-wrap">[ moleculetype ]
; Name nrexcl
CHR 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 H 1 CHR H3 1 1 1 H 0 0 ; qtot 0
2 H 1 CHR H6 2 -1 1 H 0 0 ; qtot 0
3 H 2 CHR H3 3 1 1 H 0 0 ; qtot 0
4 H 2 CHR H6 4 -1 1 H 0 0 ; qtot 0
5 H 3 CHR H3 5 1 1 H 0 0 ; qtot 0
6 H 3 CHR H6 6 -1 1 H 0 0 ; qtot 0
7 H 4 CHR H3 7 1 1 H 0 0 ; qtot 0
8 H 4 CHR H6 8 -1 1 H 0 0 ; qtot 0
9 H 5 CHR H3 9 1 1 H 0 0 ; qtot 0
10 H 5 CHR H6 10 -1 1 H 0 0 ; qtot 0
11 H 6 CHR H3 11 1 1 H 0 0 ; qtot 0
12 H 6 CHR H6 12 -1 1 H 0 0 ; qtot 0
13 H 7 CHR H3 13 1 1 H 0 0 ; qtot 0
14 H 7 CHR H6 14 -1 1 H 0 0 ; qtot 0
15 H 8 CHR H3 15 1 1 H 0 0 ; qtot 0
16 H 8 CHR H6 16 -1 1 H 0 0 ; qtot 0
17 H 9 CHR H3 17 1 1 H 0 0 ; qtot 0
18 H 9 CHR H6 18 -1 1 H 0 0 ; qtot 0
19 H 10 CHR H3 19 1 1 H 0 0 ; qtot 0
20 H 10 CHR H6 20 -1 1 H 0 0 ; qtot 0
21 H 11 CHR H3 21 1 1 H 0 0 ; qtot 0
22 H 11 CHR H6 22 -1 1 H 0 0 ; qtot 0
23 H 12 CHR H3 23 1 1 H 0 0 ; qtot 0
24 H 12 CHR H6 24 -1 1 H 0 0 ; qtot 0
25 H 13 CHR H3 25 1 1 H 0 0 ; qtot 0
26 H 13 CHR H6 26 -1 1 H 0 0 ; qtot 0
</span></div><div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="white-space:pre-wrap">Thanks,</span></div><div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px">
<span style="white-space:pre-wrap">Alex Marshall</span></div><div style="background-color:transparent;margin-top:0px;margin-left:0px;margin-bottom:0px;margin-right:0px"><span style="white-space:pre-wrap"><br>
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