[gmx-users] Methanol SOL :Number of solventmolecules = 0
Xavier Periole
X.Periole at rug.nl
Wed Dec 12 15:04:03 CET 2007
Stop the minimization at 100 steps and then equilibrate. If the
problem persists check your topology.
XAvier
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> Dear Dr. Xavier Periole,
> Thank you for guiding me through. I could solve the problem of setting up
>the system for minimization. However When started minimization run for 2000
>steps with steepest descent , I encountered yet another problem. which is as
>follows ..
> Methanol optimization:
> Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
> Removing pbc first time
> Done rmpbc
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+01
> Number of steps = 2000
> Grid: 4 x 5 x 4 cells
> calc_bor: cg0=0, cg1=553, ncg=553
> CG0[0]=0, CG1[0]=553
> CG0[1]=0, CG1[1]=0
> calc_bor: cg0=0, cg1=553, ncg=553
> CG0[0]=0, CG1[0]=553
> CG0[1]=0, CG1[1]=0
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
> Step Time Lambda
> 0 0.00000 0.00000
> calc_bor: cg0=0, cg1=553, ncg=553
> CG0[0]=0, CG1[0]=553
> CG0[1]=0, CG1[1]=0
> Program mdrun, VERSION 3.3
> Source code file: nsgrid.c, line: 226
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
> Now where do I go from here? Its asking me to energy minimize the system
>which is what I am trying to do ! What is this ci value and why is it so
>high? Kindly help me I am once again stuck. Furthermore, when I minimized
> the same peptide in SPC216 water box of 1108 water molecules for 2000 steps
>this error did not appear. When I compared the md.log files in both the cases
>I found that in case of water optimization of SPC water was enabled where as
>this line for methanol was missing which should mean that the energies are
>shooting off scale is that right ? Should I optimize my system in vacuo
>before simmulating in methanol?
> Water optimization:
> {Generated table with 500 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
> Enabling SPC water optimization for 1108 molecules.
> Initiating Steepest Descents
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest, initial mass: 3396
> Started Steepest Descents on node 0 Wed Dec 12 15:52:11 2007
> Removing pbc first time
> Done rmpbc
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+01
> Number of steps = 2000
> Going to use C-settle (1108 waters)
> wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
> rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
> Grid: 4 x 5 x 4 cells}
> regards
> sharada
>
> -- Original Message --
>From: "Xavier Periole" <X.Periole at rug.nl>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Tue, 11 Dec 2007 12:07:27 +0100
> Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules
> = 0
> in your agg2t.top you should replace the last line :
> SOL XXX
> by:
> Methanol XXX
> which is the name of the molecule.
> You should also remove the angle definition in methanol.itp. Placing
> a ";" at the beginning of the line is enough.
> XAvier
> On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
> sharada <sharada at ccmb.res.in> wrote:
>> Dear Mark Abraham,
>> I have changed MeoH to SOL in .gro and .itp files and also changed the
>>#include line to "methanol.itp"
>> It now seemed to have written the solvent molecules in the top file with SOL
>>as the name with atom types of methanol.
>> When I ran grompp program as following I get the error as shown below: I am
>>also attaching the .gro,.itp,.top files. for information. Did I miss out
>>anything ?
>> grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
>> [asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o
>>agg2_em.tpr
>>
>> Option Type Value Description
>> ------------------------------------------------------
>> -[no]h bool no Print help info and quit
>> -[no]X bool no Use dialog box GUI to edit command line options
>> -nice int 0 Set the nicelevel
>> -[no]v bool yes Be loud and noisy
>> -time real -1 Take frame at or first after this time.
>> -np int 1 Generate statusfile for # nodes
>> -[no]shuffle bool no Shuffle molecules over nodes
>> -[no]sort bool no Sort molecules according to X coordinate
>> creating statusfile for 1 node...
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
>> checking input for internal consistency...
>> calling /lib/cpp...
>> processing topology...
>> Generated 141 of the 1176 non-bonded parameter combinations
>> Excluding 3 bonded neighbours for Protein 1
>> Cleaning up temporary file grompp5RBSRX
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3
>> Source code file: toppush.c, line: 1264
>>Fatal error:
>> No such moleculetype SOL
>> -------------------------------------------------------
>> I never prefer working in root as I know the problems. Thanks for
>> suggesting. I needed to change the methanol.itp and methanol216.gro which
>>could be possible only through root.
>> regards
>> sharada
> -----------------------------------------------------
> XAvier Periole - PhD
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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