[gmx-users] eletrical filed issue

[Tong Li]

Dear Gromacs Developers or Users

I am trying to apply a constant electrical field in Gromacs. I have made a 
charged fullerene in vacuum for testing. A electrical field in x direction is 
applied as:

; Electric field
E-x = 1 2 1

However, the C60 moves only around 0.1 nm in 10 ps and then stops. My whole 
simulation period is 50 ps, in the following 40 ps, the C60 is just donging 
relaxation (likely). The first thing I have done is change the simulation step 
size from 1 fs to 0.5 fs, the simulation result is the same. Then, I have used 
the output conformation for another sequential simulation, then this happens 
again (another 0.1 nm in 10 ps). I also changed the box size to understand the 
surface effect of PBC, the difference is pretty small. The I removed the PBC, 
it didn't change, either.

I have read the manual, it says:

the first number: the number of cosines, only 1 is implemented (with frequency 
0).

However, I didn't quite get this 'frequency 0'. Does this mean there is one 
cosine in one second? Or one cosine in the whole simulation period? Or in one 
simulation time step?

Another thing is I have checked the field output, it is as below. I guess this 
means constant force field, but not quite sure.

Thanks a lot for your help!

 0   2   0   0 #FIELD
0.0005   2   0   0 #FIELD
 0.001   2   0   0 #FIELD
0.0015   2   0   0 #FIELD
 0.002   2   0   0 #FIELD
0.0025   2   0   0 #FIELD
 0.003   2   0   0 #FIELD
0.0035   2   0   0 #FIELD
 0.004   2   0   0 #FIELD
0.0045   2   0   0 #FIELD
 0.005   2   0   0 #FIELD
0.0055   2   0   0 #FIELD
 0.006   2   0   0 #FIELD
0.0065   2   0   0 #FIELD
 0.007   2   0   0 #FIELD
0.0075   2   0   0 #FIELD
 0.008   2   0   0 #FIELD
0.0085   2   0   0 #FIELD
 0.009   2   0   0 #FIELD
0.0095   2   0   0 #FIELD
  0.01   2   0   0 #FIELD
0.0105   2   0   0 #FIELD
 0.011   2   0   0 #FIELD
0.0115   2   0   0 #FIELD
 0.012   2   0   0 #FIELD
0.0125   2   0   0 #FIELD
 0.013   2   0   0 #FIELD
0.0135   2   0   0 #FIELD
 0.014   2   0   0 #FIELD
0.0145   2   0   0 #FIELD
 0.015   2   0   0 #FIELD
0.0155   2   0   0 #FIELD
 0.016   2   0   0 #FIELD
Tong Li
email t14...@qut.edu.au

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[gmx-users] g_dist problem in Implicit solvent

[Tong Li]

Dear All,

I got this problem recently. I want to use g_dist to calculate the distance 
between two group in my simulation system. However, when I use the implicit 
solvent for simulation, g_dist went into this problem: Molecule in topology has 
atom numbers below and above natoms.

I have used tpbconv to create a new tpr file, and also used gmxcheck to check 
my traj file, they are all consistent. Also, I have never run into this problem 
when I was using explicit solvent. Hence, I highly suspect this problem comes 
from the implicit solvent.

Really appreciate that you can help me go through this. Thanks a lot!

Cheers,
Tony

:-)  g_dist  (-:

Option Filename  Type Description

  -f   traj.trr  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -snowater.tpr  InputRun input file: tpr tpb tpa
  -n  index.ndx  Input, Opt!  Index file
  -o   dist.xvg  Output, Opt. xvgr/xmgr file
-lt   lifetime.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time (ps)
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-distreal   0   Print all atoms in group 2 closer than dist to
the center of mass of group 1

Reading file nowater.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 10199 elements
Group 1 (  Other) has  4372 elements
Group 2 (GRA) has  3936 elements
Group 3 (ORA) has   223 elements
Group 4 (HRA) has   213 elements
Group 5 (Protein) has  5827 elements
Group 6 (  Protein-H) has  2933 elements
Group 7 (C-alpha) has   375 elements
Group 8 (   Backbone) has  1125 elements
Group 9 (  MainChain) has  1501 elements
Group10 (   MainChain+Cb) has  1848 elements
Group11 (MainChain+H) has  1859 elements
Group12 (  SideChain) has  3968 elements
Group13 (SideChain-H) has  1432 elements
Group14 (Prot-Masses) has  5827 elements
Group15 (non-Protein) has  4372 elements
Select a group: 1
Selected 1: 'Other'
Select a group: 14
Selected 14: 'Prot-Masses'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up dist.xvg to ./#dist.xvg.1#

---
Program g_dist, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (10198).
You are probably trying to use a trajectory which does not match the first 
10198 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

There's No Room For the Weak (Joy Division)

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