<br>I get an error like this=<br>Step 43230, time 86.46 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.033583, max 1.621884 (between atoms 2032 and 2030)<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 2032 2030 90.0 0.4449 0.2622 0.1000<br> 2031 2030 90.0 0.1949 0.1264 0.1000<br>Wrote pdb files with previous and current coordinates<br>
<br>Step 43231, time 86.462 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.066301, max 3.173023 (between atoms 2032 and 2030)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
2032 2030 90.0 0.2622 0.4173 0.1000<br> 2031 2030 89.9 0.1264 0.1675 0.1000<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.5.3<br>Source code file: constr.c, line: 176<br>
<br>Fatal error:<br>Too many LINCS warnings (1001)<br>If you know what you are doing you can adjust the lincs warning threshold in your mdp file<br>or set the environment variable GMX_MAXCONSTRWARN to -1,<br>but normally it is better to fix the problem<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br>
<br><br>and my md.mdp file i altered goes like this=<br>; VARIOUS PREPROCESSING OPTIONS<br>title = Production Simulation<br>cpp = /lib/cpp<br><br>; RUN CONTROL PARAMETERS<br>integrator = md<br>
tinit = 0 ; Starting time<br>dt = 0.002 ; 2 femtosecond time step for integration<br>nsteps = 2500000 ; Make it 10 ns<br><br>; OUTPUT CONTROL OPTIONS<br>
nstxout = 500 ; Writing full precision coordinates every nanosecond<br>nstvout = 500 ; Writing velocities every nanosecond<br>nstfout = 0 ; Not writing forces<br>nstlog = 2500 ; Writing to the log file every step<br>
nstenergy = 2500 ; Writing out energy information every step<br>nstxtcout = 500 ; Writing coordinates every 5 ps<br>energygrps = Protein Non-Protein<br><br>; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 5<br>ns-type = Grid<br>pbc = xyz<br>rlist = 0.9<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>coulombtype = Reaction-Field<br>
rcoulomb = 1.4<br>epsilon_rf = 78<br>epsilon_r = 1<br>vdw-type = Cut-off<br>rvdw = 1.4<br><br>; Temperature coupling<br>Tcoupl = Berendsen<br>
tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Pressure coupling<br>Pcoupl = Berendsen<br>Pcoupltype = Isotropic<br>
tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>; OPTIONS FOR BONDS<br>constraints = all-bonds<br>
constraint-algorithm = Lincs<br>unconstrained-start = yes<br>lincs-order = 4<br>lincs-iter = 1<br>lincs-warnangle = 30<br><br><br>how should i rectify this. Please help<br><br>
<br><div class="gmail_quote">On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 19/12/2011 1:05 AM, aiswarya pawar wrote:
<blockquote type="cite">Hi users,
<div><br>
</div>
<div>I did energy minimization of a protein complex using the
following minimization mdp file.</div>
</blockquote>
<br></div>
See <a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>
for general advice.<div><div class="h5"><br>
<br>
<blockquote type="cite">
<div><br>
</div>
<div>
<div>; Lines starting with ';' ARE COMMENTS</div>
<div>; Everything following ';' is also comment</div>
<div><br>
</div>
<div>title<span style="white-space:pre-wrap">
</span>= Energy Minimization<span style="white-space:pre-wrap"> </span>; Title of run</div>
<div><br>
</div>
<div>; The following line tell the program the standard
locations where to find certain files</div>
<div>cpp<span style="white-space:pre-wrap"> </span>=
/lib/cpp<span style="white-space:pre-wrap">
</span>; Preprocessor</div>
<div><br>
</div>
<div><br>
</div>
<div>; Define can be used to control processes</div>
<div>define = -DFLEXIBLE</div>
<div><br>
</div>
<div>; Parameters describing what to do, when to stop and what
to save</div>
<div>integrator<span style="white-space:pre-wrap"> </span>= steep<span style="white-space:pre-wrap"> </span>;
Algorithm (steep = steepest descent minimization)</div>
<div>emtol<span style="white-space:pre-wrap">
</span>= 1000.0 <span style="white-space:pre-wrap"> </span>; Stop minimization when
the maximum force < 1.0 kJ/mol</div>
<div>emstep = 0.01</div>
<div>nsteps<span style="white-space:pre-wrap">
</span>= 5000<span style="white-space:pre-wrap"> </span>; Maximum number of
(minimization) steps to perform</div>
<div>nstenergy<span style="white-space:pre-wrap"> </span>= 10<span style="white-space:pre-wrap"> </span>;
Write energies to disk every nstenergy steps</div>
<div>energygrps<span style="white-space:pre-wrap"> </span>= Protein<span style="white-space:pre-wrap"> </span>;
Which energy group(s) to write to disk</div>
<div><br>
</div>
<div>; Parameters describing how to find the neighbors of each
atom and how to calculate the interactions</div>
<div>nstlist<span style="white-space:pre-wrap">
</span>= 10<span style="white-space:pre-wrap"> </span>; Frequency to update the
neighbor list and long range forces</div>
<div>ns_type<span style="white-space:pre-wrap">
</span>= grid <span style="white-space:pre-wrap"> </span>; Method to determine
neighbor list (simple, grid)</div>
<div>rlist<span style="white-space:pre-wrap">
</span>= 1.0<span style="white-space:pre-wrap"> </span>; Cut-off for making
neighbor list (short range forces)</div>
<div>coulombtype<span style="white-space:pre-wrap"> </span>= PME <span style="white-space:pre-wrap"> </span>;
Treatment of long range electrostatic interactions</div>
<div>rcoulomb<span style="white-space:pre-wrap"> </span>= 1.0<span style="white-space:pre-wrap"> </span>;
long range electrostatic cut-off</div>
<div>rvdw<span style="white-space:pre-wrap"> </span>=
1.4<span style="white-space:pre-wrap"> </span>;
long range Van der Waals cut-off</div>
<div>constraints<span style="white-space:pre-wrap"> </span>= none<span style="white-space:pre-wrap"> </span>;
Bond types to replace by constraints</div>
<div>pbc<span style="white-space:pre-wrap"> </span>
= xyz<span style="white-space:pre-wrap">
</span>; Periodic Boundary Conditions (yes/no)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>and the pr.mdp =</div>
<div><br>
</div>
<div>
<div>
<div>; VARIOUS PREPROCESSING OPTIONS</div>
<div>title = Position Restrained Molecular
Dynamics</div>
<div>define = -DPOSRES</div>
<div><br>
</div>
<div>constraints = all-bonds</div>
<div>integrator = md</div>
<div>dt = 0.001 ; ps !</div>
<div>nsteps = 25000 ; total 50 ps.</div>
<div>nstcomm = 10</div>
<div>nstxout = 500 ; collect data every 1 ps</div>
<div>nstxtcout = 500</div>
<div>nstvout = 0</div>
<div>nstfout = 0</div>
<div>nstlist = 10</div>
<div>ns_type = grid</div>
<div>rlist = 1.0</div>
<div>coulombtype = PME</div>
<div>rcoulomb = 1.0</div>
<div>vdwtype = cut-off</div>
<div>rvdw = 1.4</div>
<div>pme_order = 4</div>
<div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div>
<div>DispCorr = no</div>
<div>; Berendsen temperature coupling is on</div>
<div>Tcoupl = v-rescale</div>
<div>tau_t = 0.1 0.1</div>
<div>tc-grps = protein non-protein</div>
<div>ref_t = 300 300</div>
<div>; Pressure coupling is on</div>
<div>Pcoupl = parrinello-rahman</div>
<div>Pcoupltype = isotropic</div>
<div>tau_p = 1.0</div>
<div>compressibility = 4.5e-5</div>
<div>ref_p = 1.0</div>
<div>; Generate velocites is on at 300 K.</div>
<div>
gen_vel = yes</div>
<div>gen_temp = 300.0</div>
<div>gen_seed = -1</div>
</div>
</div>
</blockquote>
<br></div></div>
You are asking for trouble by generating velocities and doing
position restraints with P-R pressure coupling in one step. It might
work, but the workflow in the above link is safer.<div><div class="h5"><br>
<br>
<blockquote type="cite">
<div><br>
</div>
<div>and md.mdp file =</div>
<div><br>
</div>
<div>
<div>; VARIOUS PREPROCESSING OPTIONS</div>
<div>title = Position Restrained Molecular
Dynamics</div>
<div><br>
</div>
<div><br>
</div>
<div>; RUN CONTROL PARAMETERS</div>
<div>constraints = all-bonds</div>
<div>integrator = md</div>
<div>dt = 0.002 ; 2fs !</div>
<div>nsteps = 2500000 ; total 5000 ps.</div>
<div>nstcomm = 10</div>
<div>nstxout = 500 ; collect data every 1 ps</div>
<div>nstxtcout = 0</div>
<div>nstvout = 0</div>
<div>nstfout = 0</div>
<div>nstlist = 10</div>
<div>ns_type = grid</div>
<div>rlist = 1.0</div>
<div>coulombtype = PME</div>
<div>rcoulomb = 1.0</div>
<div>vdwtype = cut-off</div>
<div>rvdw = 1.4</div>
<div>pme_order = 4</div>
<div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div>
<div>DispCorr = no</div>
<div>; Berendsen temperature coupling is on</div>
<div>Tcoupl = v-rescale</div>
<div>tau_t = 0.1 0.1</div>
<div>tc-grps = protein non-protein</div>
<div>ref_t = 300 300</div>
<div>; Pressure coupling is on</div>
<div>Pcoupl = parrinello-rahman</div>
<div>Pcoupltype = isotropic</div>
<div>tau_p = 1.0</div>
<div>compressibility = 4.5e-5</div>
<div>ref_p = 1.0</div>
<div>; Generate velocites is on at 300 K.</div>
<div>gen_vel = yes</div>
<div>gen_temp = 300.0</div>
<div>gen_seed = -1</div>
</div>
</blockquote>
<br></div></div>
Why are you re-generating non-equilibrium velocities after
equilibrating them?<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote type="cite">
<div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>The minimization step went well. but while doing the final
mdrun am getting LINCS error. i read through the numerous
mailing list on grimaces but still couldn't understand how would
i fix this. am getting this error for all the 10 protein complex
i did minimization for. Please help.</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Aiswarya</div>
<div><br>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div>
<br>--<br>
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