<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
</head>
<body text="#000000" bgcolor="#ffffff">
<div class="moz-text-html" lang="x-western">
<div class="moz-text-html" lang="x-western">
<div class="moz-text-html" lang="x-western"><tt>Dear Justin,<br>
I run again the simulation, this time I keep the same thermostat </tt>(Nose-Hoover).
I
still
get
the same error <span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family: monospace;"></span></span><br>
manu.mura wrote:<br>
------------------------------------------------------------<br>
<span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family: monospace;">READ 3 BOX
VELOCITIES FROM final_NPT.edr<br>
<br>
<br>
-------------------------------------------------------<br>
Program grompp_mpi_d, VERSION 4.5.1<br>
Source code file: enxio.c, line: 1022<br>
<br>
Fatal error:<br>
Could not find energy term named 'Xi-0-Protein'<br>
---------------------------------------------------------------<br>
<br>
my input file is the following:<br>
<br>
; Run parameters<br>
integrator = md ; leap-frog integrator<br>
nsteps = 40000000 ; 2 * 500000 = 1000 ps (1 ns)<br>
dt = 0.002 ; 2 fs<br>
; Output control<br>
nstxout = 1000 ; save coordinates every 2 ps<br>
nstvout = 1000 ; save velocities every 2 ps<br>
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps<br>
nstenergy = 1000 ; save energies every 2 ps<br>
nstlog = 1000 ; update log file every 2 ps<br>
; Bond parameters<br>
continuation = yes ; Restarting after NPT <br>
constraint_algorithm = lincs ; holonomic constraints <br>
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained<br>
lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring grid cels<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.2 ; short-range neighborlist cutoff (in nm)<br>
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>
tcoupl = Nose-Hoover ; More accurate thermostat<br>
tc-grps = Protein DMP SOL ; three coupling groups - more
accurate<br>
tau_t = 0.2 0.2 0.2 ; time constant, in ps<br>
ref_t = 300 300 300 ; reference temperature, one for
each group, in K<br>
; Pressure coupling is on<br>
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>
pcoupltype = semiisotropic ; uniform scaling of x-y box
vectors, independent z<br>
tau_p = 2.0 ; time constant, in ps<br>
ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)<br>
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility,
bar^-1<br>
; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>
DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>
gen_vel = no ; Velocity generation is off<br>
; COM motion removal<br>
; These options remove motion of the protein/bilayer relative to the
solvent/ions<br>
nstcomm = 1<br>
comm-mode = Linear<br>
comm-grps = Protein_DMP SOL<br>
<br>
Thank you <br>
best regards <br>
<br>
Manuela <br>
<br>
<blockquote
style="border-left: 0.2em solid rgb(85, 85, 238); margin: 0em; padding-left: 0.85em;">
<pre style="margin: 0em;">Dear Justin,
I have the same problem.
I started with Berendsen during NPT and I switch the thermostat
(Nose-Hoover ) to run MD.
I get the following error.
Program grompp_mpi_d, VERSION 4.5.1
Source code file: enxio.c, line: 1022
Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the GROMACS
website at <a rel="nofollow"
href="http://www.gromacs.org/Documentation/Errors"
style="color: rgb(0, 0, 0);">http://www.gromacs.org/Documentation/Errors</a>
-------------------------------------------------------
I am not able to do the checkpoint file ( grompp -t *.cpt) because I get
another error.
</pre>
</blockquote>
<tt>Saying that you "get another error" is not helpful. You cannot pass
an .edr<span class="Apple-converted-space"> </span></tt><tt>file to
grompp when switching thermostats. You should be able to pass a<span
class="Apple-converted-space"> </span></tt><tt>checkpoint file to
preserve all velocities, etc. If you want further help, post<span
class="Apple-converted-space"> </span></tt><tt>the exact error
message, and perhaps your .mdp file. Otherwise, all I can say<span
class="Apple-converted-space"> </span></tt><tt>is either something
went wrong or you're doing something wrong.</tt>
<pre style="margin: 0em;">-Justin
</pre>
<blockquote
style="border-left: 0.2em solid rgb(85, 85, 238); margin: 0em; padding-left: 0.85em;">
<pre style="margin: 0em;">Could you help me.
Thank you
Best Regards
Manuela</pre>
</blockquote>
</span></span>
</div>
</div>
</div>
</body>
</html>