[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5?
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 17 16:45:07 CET 2012
qiancheng shen wrote:
> Dear David,
>
> Thank you very much.
> /* A little modification to your first post. */
> "
> grompp_d -f cg -o cg
> mdrun_d -s cg/* -o*/ conf.g96 --------------------->
> mdrun_d -s cg /*-c*/ conf.g96 (Use -o will only output *.trr)
> grompp_d -f nm -c conf.g96 -o nm
> mdrun_d -s nm
> g_nmeig_d
> "
> And when I used "integrator = nm" in *.mdp file and run "mdrun_d -s
> nm". Gromacs said "Constraints present with Normal Mode Analysis, this
> combination is not supported".
> Could give me some suggestion about that error?
>
> The commands I used is listed below:
> 1. */pdb2gmx_d -ignh -ff /*/gromos43a1 *-f* 1OMB.pdb *-water*
> spce *-o* conf.gro *-p* topol.top/
> 2. *///editconf_d -f /*/conf.gro *-o* BOX.gro *-d* 1.5/
> 3. */genbox_d -cp /*/BOX.gro *-cs* spc216 *-o* SOL *-p* topol.top/
> 4. */grompp_d -f /*/em.mdp *-c* SOL.gro *-p* topol.top *-o* em.tpr/
> 5. */mdrun_d -s /*/em.tpr *-deffnm* em *-c* tx.g96 *-v*/
> //Energy Min
> 6. /*grompp_d*/ /*-f */nm.mdp /*-c*/ tx.g96 /*-o*/ nm
> 7. /*mdrun_d*/ /*-s*/ nm -----> A fatal error "Constraints
> present with Normal Mode Analysis, this combination is not
> supported"
>
In adding solvent, these molecules are held rigid by the SETTLE algorithm, which
is a type of constraint. As the fatal error tells you, you cannot do this. See
below for more comments on em.mdp.
> /*em.mdp*/
> define = -DFLEXIBLE
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 400
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> optimize_fft = yes
> ;
> ; Energy minimizing stuff
> ;
> emtol = 1000
> emstep = 0.01
>
Steepest descents EM with this large of a maximum force is not appropriate for
running NM calculations. You need extremely thorough EM, perhaps several rounds
of it using either CG or L-BFGS (or both) to a maximal force as low as machine
precision will allow.
-Justin
> ---------------------------------------
> /*nm.mdp*/
> constraints = none
> integrator = nm
> dt = 0.002 ; ps !
> nsteps = 400
> nstlist = 10
> ns_type = grid
> rlist = 1.2
> coulombtype = PME-Switch
> rcoulomb = 1.0
> vdwtype = Cut-off
> rvdw = 1.4
>
>
> Thank you very much.
>
> Shen.
>
> 在 2012年3月17日 下午10:46，David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>写道：
>
> On 2012-03-17 15:34, qiancheng shen wrote:
>
> Dear David:
> Thank you very much!! I'm really new to Gromacs.
> I think I should use the *.trr file(from mdrun_d, energy
> minimization)
> as an input file for generating *.tpr for Normal Mode Analysis.
>
>
> Please read my previous email.
>
>
> But what the *.mdp file looks like while using "grompp_d -f nm -c
> conf.g96 -o nm" to make such *.tpr file?
>
> integrator = nm
>
> I appreciate your help.
>
> Shen
>
> 在 2012年3月17日 下午9:47，David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>>__写道：
>
>
> On 2012-03-17 14:44, qiancheng shen wrote:
>
> Hello Everyone，
> I‘m confused about Normal Mode Analysis of Gromacs. I have
> googled a lot
> but find little useful.
> I installed Gromacs 4.5.5 by CMake on Win7(Double Precision).
> Gromacs manual said "It is imperative that you use the |-t|
> option to
> |grompp
>
> <http://www.gromacs.org/____Documentation/Gromacs_____Utilities/grompp
> <http://www.gromacs.org/__Documentation/Gromacs___Utilities/grompp>
>
>
> <http://www.gromacs.org/__Documentation/Gromacs___Utilities/grompp
> <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp>>>|
>
> when you create the normal mode run input file
>
> <http://www.gromacs.org/____Documentation/File_Formats/____Topology_%28.tpr%29_File
> <http://www.gromacs.org/__Documentation/File_Formats/__Topology_%28.tpr%29_File>
>
>
> <http://www.gromacs.org/__Documentation/File_Formats/__Topology_%28.tpr%29_File
> <http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File>>>,
>
> so that you read full precision binary coordinates and
> not the
> three-decimal .gro
>
> <http://www.gromacs.org/____Documentation/File_Formats/.____gro_File
> <http://www.gromacs.org/__Documentation/File_Formats/.__gro_File>
>
>
> <http://www.gromacs.org/__Documentation/File_Formats/.__gro_File
> <http://www.gromacs.org/Documentation/File_Formats/.gro_File>>>
> file." But
>
> I don't exactly what it means....
> Could anyone give me a step-by-step example?
>
> Thanks in advance.
>
> shen
>
>
> grompp_d -f cg -o cg
> mdrun_d -s cg -o conf.g96
> grompp_d -f nm -c conf.g96 -o nm
> mdrun_d -s nm
> g_nmeig_d
>
> You can use the g96 coordinate format instead of using the
> trr file
> from the conjugate gradients energy minimization.
> Set all cut-offs to zero (= infinite).
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
>
> http://folding.bmc.uu.se
> --
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> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> http://folding.bmc.uu.se
> --
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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