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Of course.
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<p style="margin: 0px;">I am trying to run the ribosome 30s subunit on gromax 4.5. I chose the AMBER force field since it had the least issues with RNA and that made running pdb2gmx much easier. Everything is fine till I run a md. Below I have attached everything I think is informative. I have run a purely protein md with GROMOS96-43a1 and had no problems, but once I try to run this under AMBER03 it fails with LINCS errors.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><strong>energy minimization mdp file:</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">cpp                 =  /usr/bin/cpp<br />
define              =  -DFLEX_SPC<br />
constraints         =  none<br />
integrator          =  steep<br />
nsteps              =  5000<br />
;<br />
;       Energy minimizing stuff<br />
;<br />
emtol               =  200<br />
emstep              =  0.01<br />
<br />
nstcomm             =  1<br />
ns_type             =  grid<br />
rlist               =  1<br />
rcoulomb            =  1.0<br />
rvdw                =  1.0<br />
Tcoupl              =  no<br />
Pcoupl              =  no<br />
gen_vel             =  no</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><strong>Positional restraint mdp file:</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">define                  = -DPOSRES<br />
constraints             = all-bonds<br />
integrator              = md<br />
dt                      = 0.004 ; ps<br />
nsteps                  = 2500 ; total ps = dt*nsteps<br />
nstcomm                 = 1<br />
nstxout                 = 200 ; output coordinates every ps = dt*nstxout<br />
nstvout                 = 1000 ; output velocities every ps = dt*nstvout<br />
nstfout                 = 0<br />
nstenergy               = 10<br />
nstlog                  = 10<br />
nstlist                 = 10<br />
ns_type                 = grid<br />
rlist                   = 0.9<br />
coulombtype             = PME<br />
rcoulomb                = 0.9<br />
rvdw                    = 1.0<br />
fourierspacing          = 0.12<br />
fourier_nx              = 0<br />
fourier_ny              = 0<br />
fourier_nz              = 0<br />
pme_order               = 6<br />
ewald_rtol              = 1e-5<br />
optimize_fft            = yes<br />
; Berendsen temperature coupling is on<br />
Tcoupl                  = v-rescale<br />
tau_t                   = 0.1       0.1  0.1   0.1   0.1<br />
tc_grps                 = protein   RNA  SOL   NA    CL<br />
ref_t                   = 310       310  310   310   310<br />
; Pressure coupling is on<br />
pcoupl                  = berendsen<br />
pcoupltype              = isotropic<br />
tau_p                   = 0.5<br />
compressibility         = 4.5e-5<br />
ref_p                   = 1.0<br />
; Generate velocities is on at 310K (core body temp)<br />
gen_vel                 = yes<br />
gen_temp                = 310.0<br />
gen_seed                = 173529</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><strong>main molecular dynamics mdp file:</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">define                  = -DPOSRES<br />
constraints             = all-bonds<br />
integrator              = md<br />
dt                      = 0.004 ; ps<br />
nsteps                  = 25000 ; total ps = dt*nsteps<br />
nstcomm                 = 1<br />
nstxout                 = 200 ; output coordinates every ps = dt*nstxout<br />
nstvout                 = 1000 ; output velocities every ps = dt*nstvout<br />
nstfout                 = 0<br />
nstenergy               = 10<br />
nstlog                  = 10<br />
nstlist                 = 10<br />
ns_type                 = grid<br />
rlist                   = 0.9<br />
coulombtype             = PME<br />
rcoulomb                = 0.9<br />
rvdw                    = 1.0<br />
fourierspacing          = 0.12<br />
fourier_nx              = 0<br />
fourier_ny              = 0<br />
fourier_nz              = 0<br />
pme_order               = 6<br />
ewald_rtol              = 1e-5<br />
optimize_fft            = yes<br />
; Berendsen temperature coupling is on<br />
Tcoupl                  = v-rescale<br />
tau_t                   = 0.1       0.1  0.1   0.1   0.1<br />
tc_grps                 = protein   RNA  SOL   NA    CL<br />
ref_t                   = 310       310  310   310   310<br />
; Pressure coupling is on<br />
pcoupl                  = berendsen</p>
<p style="margin: 0px;">pcoupltype              = isotropic</p>
<p style="margin: 0px;">tau_p                   = 0.5<br />
compressibility         = 4.5e-5<br />
ref_p                   = 1.0<br />
; Generate velocities is on at 310K (core body temp)<br />
gen_vel                 = yes<br />
gen_temp                = 310.0<br />
gen_seed                = 173529</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><strong>And my script for running the whole process:</strong></p>
<br />
<br />
pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top<br />
<br />
<p style="margin: 0px;">editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5<br />
<br />
genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top<br />
<br />
grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr<br />
<br />
genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001 -pname NA -nname CL -g receptor_ion.log -p receptor.top</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><strong>Here I select the SOL for ions...</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr<br />
<br />
mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log<br />
<br />
grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr<br />
<br />
mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt<br />
<br />
grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr<br />
<br />
mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt<br />
<br />
<strong>Where receptor is of course my protein/RNA pdb name</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I always make sure that the pdb doesn't give me notes or warnings or errors of course in the pdb2gmx step. Most of the time I minimize to my computers "machine precision."</p>
<p style="margin: 0px;"><strong></strong></p>
<p style="margin: 0px;"><strong>This is the return I get from the "EM" step:</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Stepsize too small, or no change in energy.<br />
Converged to machine precision,<br />
but not to the requested precision Fmax < 200<br />
<br />
Double precision normally gives you higher accuracy.<br />
You might need to increase your constraint accuracy, or turn<br />
off constraints alltogether (set constraints = none in mdp file)<br />
<br />
writing lowest energy coordinates.<br />
<br />
Steepest Descents converged to machine precision in 324 steps,<br />
but did not reach the requested Fmax < 200.<br />
Potential Energy  = -1.9868888e+07<br />
Maximum force     =  8.7276396e+03 on atom 19080<br />
Norm of force     =  3.8592850e+01</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><strong>I will get this error sometime in the "PR" step of my script:</strong></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">step 0<br />
Step 11  Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087<br />
<br />
Step 11  Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087<br />
<br />
Step 21  Warning: pressure scaling more than 1%, mu: 0.849053 0.849053 0.849053<br />
<br />
Step 21  Warning: pressure scaling more than 1%, mu: 0.849053 0.849053 0.849053<br />
<br />
Step 22, time 0.088 (ps)  LINCS WARNING<br />
relative constraint deviation after LINCS:<br />
rms 0.005723, max 0.026407 (between atoms 6545 and 6542)<br />
bonds that rotated more than 30 degrees:<br />
 atom 1 atom 2  angle  previous, current, constraint length</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I hope this is enough information (and not to lengthy). Any help would be much appreciated.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu<br />
Cell: 509-879-4173</p>
<p style="margin: 0px;"><span></span></p>
<div style="margin: 5px 0px;">
On September 9, 2010 at 9:11 PM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> > First off I am using gromacs 4.5. I will also post all of my files and<br />
> > errors if they help.<br />
> ><br />
> > <br />
> ><br />
> > If I run a protein in GROMOS96 all my md runs complete succesfully. But<br />
> > if I change to any of the AMBER force fields I get LINCS errors in my<br />
> > positional restraint md run. I have tried using shake, 1 fs step sizes,<br />
> > -heavyh, and many more. Does anyone know what is going on here?<br />
> ><br />
><br />
> A complete (but not overly lengthy) post will save everyone a lot of time.<br />
> Based on the information you've provided here, I see now way to diagnose the<br />
> problem.  The most important information to post would be your .mdp file.<br />
> Certain settings can influence stability.  A description of the hardware,<br />
> compilers used, etc. can also be useful.<br />
><br />
> -Justin<br />
><br />
> > <br />
> ><br />
> > The reason I want to use AMBER is the fact that I want to run md on the<br />
> > 30s rybosome and amber converts RNA much easier than GROMOS force fields.<br />
> ><br />
> > <br />
> ><br />
> > <br />
> ><br />
> > Thank you in advance,<br />
> ><br />
> > <br />
> ><br />
> > TJ Mustard Email: mustardt@onid.orst.edu<br />
> > Cell: 509-879-4173<br />
> ><br />
> > <br />
> ><br />
> ><br />
><br />
> --<br />
> ========================================<br />
><br />
> Justin A. Lemkul<br />
> Ph.D. Candidate<br />
> ICTAS Doctoral Scholar<br />
> MILES-IGERT Trainee<br />
> Department of Biochemistry<br />
> Virginia Tech<br />
> Blacksburg, VA<br />
> jalemkul[at]vt.edu | (540) 231-9080<br />
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br />
><br />
> ========================================<br />
> --<br />
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><br />
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