[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion

[Simple]

   In chemical experiments that ion effect is important,tetramethylammonium 
(TMA) is usually added to compensate the ion strength.I would like to test it 
in simulation. There were experiments showed that the ion contributed a lot 
to the distinct results.
   I looked around but not found a topology  of TMA is ready-to-use. So I 
decided to create one. Thanks for  Schuettelkopf and  van Aalten, The PRODRG 
server do all the things. Since I am still a newbie for Gromacs and not very 
confident with my chemistry knowledge,I wonder if the parameters in the 
topology is rational? (The topology is present at the last.)

   The second problem is how can I use this topology as a general ion. 
   It is difficult to add them into gro file by hand because I should put a 
lot of TMA into the solutions.
   If I can treat it as a general ion, such as Na or Mg,etc, which will save 
me a lot. My straight forward thought is to add the information into the 
ion.itp, so genion can find and use it. If this work, I believe others would 
also benefit from it, since TMA is so widely used. Does it work well?
   If this method is not so good,I think I can write a simple program to 
substitute the ion in the gro with TMA. Of course, I would rewrite the 
position of all the TMA atom and renumber the atom. For the top file, I need 
only replace the ion name with TMA.
   What should I pay a lot of attention to for these method?

   If something I wrote are totally wrong, please not hesitate to let me know. 
Thanks.

topology created by PRODRG 
;   
;   This file was generated by PRODRG version 051202.0518
;   PRODRG written/copyrighted by Daan van Aalten
;   
;   Questions/comments to [EMAIL PROTECTED]
;   
;   When using this software in a publication, cite:
;   A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;   PRODRG - a tool for high-throughput crystallography
;   of protein-ligand complexes.
;   Acta Crystallogr. D60, 1355--1363.
;   
;   

[ moleculetype ]
; Name nrexcl
TMA  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1   CH3 1  TMA  C1 10.076  15.0350   
 2NL 1  TMA  N1 10.696  14.0067   
 3   CH3 1  TMA  C3 10.076  15.0350   
 4   CH3 1  TMA  C4 10.076  15.0350   
 5   CH3 1  TMA  C2 10.076  15.0350   

[ bonds ]
; ai  aj  fuc0, c1, ...
   1   2   10.147376560.00.147376560.0 ;C1   N1   
   2   3   10.147376560.00.147376560.0 ;N1   C3   
   2   4   10.147376560.00.147376560.0 ;N1   C4   
   2   5   10.147376560.00.147376560.0 ;N1   C2   

[ pairs ]
; ai  aj  fuc0, c1, ...

[ angles ]
; ai  aj  ak  fuc0, c1, ...
   1   2   3   1109.5   376.6109.5   376.6 ;C1   N1   C3   
   1   2   4   1109.5   376.6109.5   376.6 ;C1   N1   C4   
   1   2   5   1109.5   376.6109.5   376.6 ;C1   N1   C2   
   3   2   4   1109.5   376.6109.5   376.6 ;C3   N1   C4   
   3   2   5   1109.5   376.6109.5   376.6 ;C3   N1   C2   
   4   2   5   1109.5   376.6109.5   376.6 ;C4   N1   C2   

[ dihedrals ]
; ai  aj  ak  al  fuc0, c1, m, ...
   2   1   3   4   2 35.3  836.8   35.3  836.8   ; impN1   C1   C3  
 
C4   
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[gmx-users] new rtp file generation

[안세나]

Dear gmx-usr
 
I would like to make *.top with the myoglobin pdb file which contain CO ligand like this form.
 
HETATM 1268  C   CMO   155  35.753   5.930  11.242  0.77 12.30 1MLF1367HETATM 1269  O   CMO   155  35.946   6.791  11.935  0.77 12.70 1MLF1368
 
However, this pdb file regards CO ligand as CMO residue, so I  added the information
for CMO residue to ffG43a1.rtp (I used 0 forcefield.) like this.
 
[CMO]
   [atoms]
    C C 0.383  0
O O   -0.383  0
   [bonds]
    C O
And, I also added CMO residue to aminoacids.dat.
 
But, the result of pdb2gmx said "Atom CA cannot found in residue CMO156 while adding hydrogen.
 
What's the problem?
Is it right to use rtp file, if not,  should I make *.itp file regarding CO ligand as a molecule?
Please tell me the answer. Thank you.
 
Bye,  
Sena
 
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[gmx-users] [RE]Welcome to the "gmx-users" mailing list (Digest mode)

[안세나]

 [ 원 본 메 세 지 ] ---

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[gmx-users] [RE]Welcome to the "gmx-users" mailing list (Digest mode)

[안세나]

 [ 원 본 메 세 지 ] ---

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제 목 : Welcome to the "gmx-users" mailing list (Digest mode)Welcome to the gmx-users@gromacs.org mailing list!To post to this list, send your email to:gmx-users@gromacs.orgGeneral information about the mailing list is at:http://www.gromacs.org/mailman/listinfo/gmx-usersIf you ever want to unsubscribe or change your options (eg, switch toor from digest mode, change your password, etc.), visit yoursubscription page at:http://www.gromacs.org/mailman/options/gmx-users/praise%40kaist.ac.krYou can also make such adjustments via email by sending a message to:[EMAIL PROTECTED]with the word `help' in the subject or body (don't include thequotes), and you will get back a message with instructions.You must know your password to change your options (including changingthe password, itself) or to unsubscribe. It is:1234Normally, Mailman will remind you of your gromacs.org mailing listpasswords once every month, although you can disable this if youprefer. This reminder will also include instructions on how tounsubscribe or change your account options. There is also a button onyour options page that will email your current password to you.
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[gmx-users] GAFF

[日産化学 石川誠]

Hi all,

I'm searching forecefield for a small molecule.
Dose anyone know how to get GAFF for GROMACS?

Thank you for your time.

MAKOTO ISHIKAWA


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[gmx-users] oplsaa2005?

[rob yang]

Hi list,
Just wondering if anybody have gromacs-formatted oplsaa2005 parameters? 
Thank you.


Rob


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[gmx-users] Problem with phenylglycine MD

[Ashutosh Jogalekar]

Hello
I am trying to run an MD on a short tripeptide contaning phenyglycine  
(PHG)- that is with the phenyl ring direct attached to the alpha  
carbon. I am using the OPLS force field. The peptide is (PHE-PHG-LEU)
I modified the .rtp and .hdb files accordingly. I put in the atoms,  
bonds, and improper dihedrals in the .rtp file. I put in the new name  
PHG in the aminoacids.dat file.
Everything seems to start ok, until I am done with the energy  
minimization. There is no error, and the minimization ends smoothly.  
However, at the end, the alpha carbon is distorted; it's not  
tetrahedral and the hydrogen bends towards the phenyl ring. Not  
suprisingly, in the rest of the simulation, the distortion is not  
relieved. I don't know what's going wrong, since there is no error as  
such and the .rtp and the .hdb files have been modified in an apt  
manner.
One thing is that there are no parameters for some of the dihedrals  
in the OPLS force field. So when I am doing grompp for the EM, the  
program naturally puts zeros in front of those dihedrals. Two  
examples are:

N  CA  CG CD1
HA CA CG CD1

Could this be causing the carbon to distort? If so, where can I get  
the parameters for these dihedrals?
Help will be really appreciated since I am stuck with this problem  
for days!

Thanks
Ashutosh Jogalekar
Emory University, Atlanta, GA
USA
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Re: [gmx-users] pull.pdo AFM force

[Emily Walton]

Hi all
I have a short question.  Could you please tell me what do the  
columns in pull.pdo (output file from AFM) stand for.  Is there a  
simple way to obtain forces from AFM pulling? Thank you for help.

Michal




As an example, with one pulling group, and pulling in 3D, the output  
columns read:


Time, Reference group X, Reference group Y, Reference group Z, Pull  
Group X, Pull Group Y, Pull Group Z, Spring X, Spring Y, Spring Z


for a total of 10 columns.

If you didn't pull in 3D, you'll only get output for the dimensions  
where pulldim was set to Y in your .ppa file. I'm not sure how  
multiple pull groups are handled.


I have a script to calculate the forces for pull runs using only one  
pull group in 3 dimensions that I can share on request.


-Emily Walton
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Re: [gmx-users] Range Checking Error

[David van der Spoel]

Gaurav Chopra wrote:

/ />/ />/ />/ 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.
/>/ /Please follow the advice in the above two sentences. Check your 
structure.
/>/ />/ I did the energy minimization by increasing the number of steps 
using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
/>/ and steep using -DFLEXIBLE in my mdp file and I was able to compute 
using mdrun but I got the following in my log file

/>/ />/ 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: 24594
/>/ Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
/>/ Removing pbc first time
/>/ Done rmpbc
/>/ Steepest Descents:
/>/Tolerance (Fmax)   =  1.0e+01
/>/Number of steps=1
/>/ Grid: 10 x 10 x 20 cells
/>/ Configuring nonbonded kernels...
/>/ Testing AMD 3DNow support... not present.
/>/ Testing ia32 SSE support... present.
/>/ />/ />/ Then with this when I do position restrained md, using 
-DPOSRES in mdp file for grompp and md integrator and then mdrun for 
position restrained

/>/ I get the following
/>/ />/ Step 0, time 0 (ps)  LINCS WARNING
/>/ relative constraint deviation after LINCS:
/>/ max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00

/>/ bonds that rotated more than 30 degrees:
/
turn off the constraints






Hi David

I did turn off the constraints and also made the starting structure 
unconstarined in the mdp file. The mdrun for position restrained gives 
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the 
earlier mail which has to be reviewed by the moderator of gmx list.


Thanks
Gaurav


---
Input Parameters:
  integrator   = md
  nsteps   = 1000
  init_step= 0
  ns_type  = Grid
  nstlist  = 10
  ndelta   = 2
  bDomDecomp   = FALSE
  decomp_dir   = 0
  nstcomm  = 1
  comm_mode= Linear
  nstcheckpoint= 1000
  nstlog   = 1
  nstxout  = 0
  nstvout  = 250
  nstfout  = 0
  nstenergy= 250
  nstxtcout= 250
  init_t   = 0
  delta_t  = 0.002
  xtcprec  = 1000
  nkx  = 42
  nky  = 42
  nkz  = 84
  pme_order= 4
  ewald_rtol   = 1e-05
  ewald_geometry   = 0
  epsilon_surface  = 0
  optimize_fft = FALSE
  ePBC = xyz
  bUncStart= TRUE
  bShakeSOR= FALSE
  etc  = Berendsen
  epc  = Berendsen
  epctype  = Isotropic
  tau_p= 20
  ref_p (3x3):
 ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}
 ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
 ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
  compress (3x3):
 compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
 compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
 compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}
  andersen_seed= 815131
  rlist= 1
  coulombtype  = PME
  rcoulomb_switch  = 0
  rcoulomb = 1
  vdwtype  = Cut-off
  rvdw_switch  = 0
  rvdw = 1
  epsilon_r= 1
  epsilon_rf   = 1
  tabext   = 1
  gb_algorithm = Still
  nstgbradii   = 1
  rgbradii = 2
  gb_saltconc  = 0
  implicit_solvent = No
  DispCorr = No
  fudgeQQ  = 0.5


set this to 1.0 or remove this setting



  free_energy  = no
  init_lambda  = 0
  sc_alpha = 0
  sc_power = 1
  sc_sigma = 0.3
  delta_lambda = 0
  disre_weighting  = Conservative
  disre_mixed  = FALSE
  dr_fc= 1000
  dr_tau   = 0
  nstdisreout  = 100
  orires_fc= 0
  orires_tau   = 0
  nstorireout  = 100
  dihre-fc = 1000
  dihre-tau= 0
  nstdihreout  = 100
  em_stepsize  = 0.01
  em_tol   = 10
  niter= 20
  fc_stepsize  = 0
  nstcgsteep   = 1000
  n

[gmx-users] pull.pdo AFM force

[Michal Kolinski]

Hi allI have a short question.  Could you 
please tell me what do the columns in pull.pdo (output file from AFM) stand 
for.  Is there a simple way to obtain forces from AFM pulling? Thank you 
for help.Michal  
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Re: [gmx-users] Re: LINCS Warning using mdrun

[Steffen Wolf]

---
Hi

I used the initial minimization run using grompp and mdrun using 
steepest descent for 400 steps and 0.002 ps as the step size. The 
constraints are all-atom.


The following is the output from the log file that was generated after 
the md.

Any suggestions?

Thanks
Was the system already completely munimized, i.e. has it reached 
convergence? 400 steps seems a bit small to me. I usually had problems 
with the constraints when the system had some kind of "point of frition" 
where a bad contact was still existing. Did you check which where the 
atoms mentioned by the lincs warning or if there were bad angles or 
contacts in the starting structure?

--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany


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Re: [gmx-users] Re: LINCS Warning using mdrun

[Yang Ye]

Hi, Gaurav

Try to use another gen_seed number.

Yang Ye

Gaurav Chopra wrote:

/ Hi

/>/
/>/ I get the following error when using mdrun for a protein in 
solution. />/ I have checked the structure and everything looks fine 
to me. Could />/ you suggested anything else I could do. /
How did you energy minimze your structure? What was the output of 
mdrun during energy minization, especially the last line with Fmax, 
Epot etc.?


I should look like this:

Step=   48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, 
atom= 78754
Step=   49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, 
atom= 13032
Step=   50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, 
atom= 13032


Jochen

Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And 
have you run a minimization before starting the simulation?

hear from you soon
Steffen


---
Hi

I used the initial minimization run using grompp and mdrun using 
steepest descent for 400 steps and 0.002 ps as the step size. The 
constraints are all-atom.


The following is the output from the log file that was generated after 
the md.

Any suggestions?

Thanks

Gaurav

---   mdrun log file output --

Initializing LINear Constraint Solver
 number of constraints is 934
 average number of constraints coupled to one constraint is 3.6

  Rel. Constraint Deviation:  Maxbetween atoms RMS
  Before LINCS 0.608377894898   0.031756
   After LINCS 0.126305892894   0.007000


Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   898899   41.60.1015   0.0997  0.1010
   898900   38.10.1038   0.0984  0.1010
Going to use C-settle (6845 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 
0.00646074

rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)
  Rel. Constraint Deviation:  Maxbetween atoms RMS
  Before LINCS 0.115310685686   0.023558
   After LINCS 0.115624892894   0.006694

Started mdrun on node 0 Tue Mar 14 04:21:35 2006
Initial temperature: 299.541 K
  Step   Time Lambda
 00.00.0

Grid: 12 x 12 x 12 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


There are 21469 atoms in your xtc output selection
  Rel. Constraint Deviation:  Maxbetween atoms RMS
  Before LINCS 10.170899898899   0.711794
   After LINCS 3.372058894895   0.239340


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   883886   36.70.1540   0.2007  0.1529
   886887   36.80.1098   0.1474  0.1090
   886888   43.60.1099   0.1575  0.1090
   886889   51.70.1526   0.2510  0.1529
   889890   60.60.1097   0.1917  0.1090
   889891   66.20.1096   0.2043  0.1090
   889892   44.60.1561   0.0485  0.1463
   892893   55.70.1042   0.1304  0.1010
   894895   54.60.1221   0.5859  0.1340
   894898  135.90.1495   0.4473  0.1340
   895896   77.60.1051   0.0671  0.1010
   895897   40.40.1011   0.1018  0.1010
   898899   40.00.0997   0.3249  0.1010
   903905   40.20.1453   0.1959  0.1449
   905906   45.20.1093   0.1556  0.1090
   905907   65.60.1542   0.3041  0.1529
   905921   35.00.1527   0.1990  0.1522
   907908   83.40.1099   0.2156  0.1090
   907909   70.10.1099   0.1907  0.1090
   907910   43.60.1519   0.1400  0.1510
   910911   77.90.1408   0.3459  0.1400
   910913   77.50.1407   0.3356  0.1400
   911912   80.80.1084   0.2512  0.1080
   911915   74.90.1405   0.2010  0.1400
   913914   81.80.1084   0.2760  0.1080
   913917   65.80.1404   0.1278  0.1400
   915916   81.70.1082   0.2186  0.1080
   915919   41.00.1402   0.1786  0.1400
   917918   82.90.1082   0.2569  0.1080
   917919   32.70.1402   0.1652  0.1400
   919920   82.30.1082   0.1984  0.1080
Constraint error in algorithm Lincs at step 0
  Energies (kJ/mol)
 AngleProper Dih. Ryckaert-Bell.  LJ-14 
Coulomb-14
   2.38010e+034.15026e+018.53343e+021.45562e+03
4.52843e+03
   LJ (SR)   Coulomb (SR

Re: [gmx-users] Re: LINCS Warning using mdrun

[Jochen Hub]

Gaurav Chopra wrote:


/ Hi


/>/
/>/ I get the following error when using mdrun for a protein in 
solution. />/ I have checked the structure and everything looks fine 
to me. Could />/ you suggested anything else I could do. /
How did you energy minimze your structure? What was the output of 
mdrun during energy minization, especially the last line with Fmax, 
Epot etc.?


I should look like this:

Step=   48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, 
atom= 78754
Step=   49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, 
atom= 13032
Step=   50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, 
atom= 13032


Jochen

Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And 
have you run a minimization before starting the simulation?

hear from you soon
Steffen


---
Hi

I used the initial minimization run using grompp and mdrun using 
steepest descent for 400 steps and 0.002 ps as the step size. The 
constraints are all-atom.


The following is the output from the log file that was generated after 
the md.

Any suggestions?

Thanks

Gaurav

---   mdrun log file output --

Better show us the output of your energy minimization. The ouput of your 
md only shows that your sctructure has some serious problem...like your 
box is too small or whatever...


Jochen



--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de



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[gmx-users] Re: LINCS Warning using mdrun

[Gaurav Chopra]

Gaurav Chopra wrote:


/ Hi



/>/
/>/ I get the following error when using mdrun for a protein in 
solution. />/ I have checked the structure and everything looks fine 
to me. Could />/ you suggested anything else I could do. /
How did you energy minimze your structure? What was the output of 
mdrun during energy minization, especially the last line with Fmax, 
Epot etc.?


I should look like this:

Step=   48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, 
atom= 78754
Step=   49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, 
atom= 13032
Step=   50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, 
atom= 13032


Jochen

Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And 
have you run a minimization before starting the simulation?

hear from you soon
Steffen


Hi

For the initial mdrun, (i.e. energy min before the actual md) the log 
file output (last part is). After this em step I use grompp with my 
final mdp file and then mdrun where I get the LINCS error.


Thanks
gaurav

Energies (kJ/mol)
 Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
  3.35740e+031.35497e+034.60212e+018.38627e+021.33998e+03
   Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
  4.11813e+035.16092e+04   -3.42126e+05   -3.63260e+04   -3.15787e+05
  Kinetic En.   Total EnergyTemperature Pressure (bar)
  0.0e+000.0e+000.0e+000.0e+00

 Step   Time Lambda
  165  165.00.0

 Step   Time Lambda
  166  166.00.0

 Step   Time Lambda
  167  167.00.0

 Energies (kJ/mol)
 Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
  3.35747e+031.35504e+034.60229e+018.38637e+021.33998e+03
   Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
  4.11748e+035.16092e+04   -3.42126e+05   -3.63260e+04   -3.15788e+05
  Kinetic En.   Total EnergyTemperature Pressure (bar)
  0.0e+000.0e+000.0e+000.0e+00

 Step   Time Lambda
  168  168.00.0

 Step   Time Lambda
  169  169.00.0

 Step   Time Lambda
  170  170.00.0


Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 171 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -3.1578772e+05
Maximum force =  5.0164816e+04 on atom 897
Norm of force =  1.1000233e+05

  M E G A - F L O P S   A C C O U N T I N G

 RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
 T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
 NF=No Forces

Computing:M-Number M-Flops  % of Flops
---
Coul(T)  20.674176  868.315392 1.8
Coul(T) [W3]  0.311534   38.941750 0.1
Coul(T) + LJ 19.239903 1058.194665 2.2
Coul(T) + LJ [W3] 3.200326  441.644988 0.9
Coul(T) + LJ [W3-W3] 78.69923730063.10853462.8
Outer nonbonded loop  8.258931   82.589310 0.2
1,4 nonbonded interactions0.413991   37.259190 0.1
Spread Q Bspline234.956736  469.913472 1.0
Gather F Bspline234.956736 2819.480832 5.9
3D-FFT  723.824532 5790.59625612.1
Solve PME10.687500  684.00 1.4
NS-Pairs214.955143 4514.058003 9.4
Reset In Box  3.671199   33.040791 0.1
Shift-X   3.670515   22.023090 0.0
CG-CoM1.225386   35.536194 0.1
Bonds 0.1597146.867702 0.0
Angles0.287622   46.882386 0.1
Propers   0.0307807.048620 0.0
RB-Dihedrals  0.320625   79.194375 0.2
Settle2.340990  756.139770 1.6
---
Total 47854.835320   100.0
---

 NODE (s)   Real (s)  (%)
 Time: 50.000 50.000100.0
Finished mdrun on node 0 Wed Mar  8 06:13:35 2006

_

Re: [gmx-users] xtc files

[YOLANDA SMALL]

Thanks David,
That works!

On Tue, 14 Mar 2006 08:49:43 +0100, David van der Spoel wrote:

> YOLANDA SMALL wrote:
> > Hi All,
> > 
> > How do I convert xtc files exported for a subset of atoms in my system to
pdb
> > files?
> > 
> > When I run trjconv, I get the following error message:
> > 
> > Fatal error: Index[0] 3611 is larger than the number of atoms in the
trajectory
> > file (3152)
> > 
> > In my mdp file I specify the option 'xtc_grps' to export a subset of solvent
and
> > protein atoms to an xtc file. This subset of atoms is defined in my index
file
> > and contains 3152 atoms. Then I discard the .trr files to save space.  It
looks
> > like the atom index gets renumbered from 1 in the new .xtc file so that the
new
> > atom indeces no longer correspond to the atoms in the original coordinate
file.
> >  How do I recover the coordinates with matching atom names from the .xtc
file?
> > 
> Sorry I misread your question.
> You make a pdb file from your original tpr using the same index group 
> you used for the xtc-grps, then you use this pdb file as reference for 
> trjconv on the xtc to pdb conversion.
> > Thanks,
> > Yolanda
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to [EMAIL PROTECTED]
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> 
> 
> -- 
> David.
> 
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
> 
> ___
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> 


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[gmx-users] Re: LINCS Warning using mdrun

[Gaurav Chopra]

/ Hi

/>/
/>/ I get the following error when using mdrun for a protein in solution. 
/>/ I have checked the structure and everything looks fine to me. Could 
/>/ you suggested anything else I could do. 
/
How did you energy minimze your structure? What was the output of mdrun 
during energy minization, especially the last line with Fmax, Epot etc.?


I should look like this:

Step=   48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, 
atom= 78754
Step=   49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, 
atom= 13032
Step=   50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, 
atom= 13032


Jochen

Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And 
have you run a minimization before starting the simulation?

hear from you soon
Steffen


---
Hi

I used the initial minimization run using grompp and mdrun using steepest 
descent for 400 steps and 0.002 ps as the step size. The constraints are 
all-atom.

The following is the output from the log file that was generated after the md. 


Any suggestions?

Thanks

Gaurav

---   mdrun log file output --

Initializing LINear Constraint Solver
 number of constraints is 934
 average number of constraints coupled to one constraint is 3.6

  Rel. Constraint Deviation:  Maxbetween atoms RMS
  Before LINCS 0.608377894898   0.031756
   After LINCS 0.126305892894   0.007000


Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   898899   41.60.1015   0.0997  0.1010
   898900   38.10.1038   0.0984  0.1010
Going to use C-settle (6845 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)
  Rel. Constraint Deviation:  Maxbetween atoms RMS
  Before LINCS 0.115310685686   0.023558
   After LINCS 0.115624892894   0.006694

Started mdrun on node 0 Tue Mar 14 04:21:35 2006
Initial temperature: 299.541 K
  Step   Time Lambda
 00.00.0

Grid: 12 x 12 x 12 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


There are 21469 atoms in your xtc output selection
  Rel. Constraint Deviation:  Maxbetween atoms RMS
  Before LINCS 10.170899898899   0.711794
   After LINCS 3.372058894895   0.239340


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   883886   36.70.1540   0.2007  0.1529
   886887   36.80.1098   0.1474  0.1090
   886888   43.60.1099   0.1575  0.1090
   886889   51.70.1526   0.2510  0.1529
   889890   60.60.1097   0.1917  0.1090
   889891   66.20.1096   0.2043  0.1090
   889892   44.60.1561   0.0485  0.1463
   892893   55.70.1042   0.1304  0.1010
   894895   54.60.1221   0.5859  0.1340
   894898  135.90.1495   0.4473  0.1340
   895896   77.60.1051   0.0671  0.1010
   895897   40.40.1011   0.1018  0.1010
   898899   40.00.0997   0.3249  0.1010
   903905   40.20.1453   0.1959  0.1449
   905906   45.20.1093   0.1556  0.1090
   905907   65.60.1542   0.3041  0.1529
   905921   35.00.1527   0.1990  0.1522
   907908   83.40.1099   0.2156  0.1090
   907909   70.10.1099   0.1907  0.1090
   907910   43.60.1519   0.1400  0.1510
   910911   77.90.1408   0.3459  0.1400
   910913   77.50.1407   0.3356  0.1400
   911912   80.80.1084   0.2512  0.1080
   911915   74.90.1405   0.2010  0.1400
   913914   81.80.1084   0.2760  0.1080
   913917   65.80.1404   0.1278  0.1400
   915916   81.70.1082   0.2186  0.1080
   915919   41.00.1402   0.1786  0.1400
   917918   82.90.1082   0.2569  0.1080
   917919   32.70.1402   0.1652  0.1400
   919920   82.30.1082   0.1984  0.1080
Constraint error in algorithm Lincs at step 0
  Energies (kJ/mol)
 AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
   2.38010e+034.15026e+018.53343e+021.45562e+034.52843e+03
   LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
   1.78128e+05   -3.41925e+05   -3.63

Re: [gmx-users] Parameters for OPLS

[Jochen Hub]

Kobi wrote:


Hello,

I'm equilibrating a Barnase/Barstar complex using OLPS Force Field, but 
I'm not sure which parameters I should use for PME. at the moment I'm 
using the following parameters:


coulombtype = PME
fourierspacing = 0.12
pme_order = 4
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0

Temperature Coupling ist turne on (berendsen) and Pressure Coupling is 
turend off. The size of the box is  4x5.8x10 nm.


thanks 
Kobi


 



These are pretty much standart parameters, so they should be fine...

--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de



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Re: [gmx-users] LINCS Warning using mdrun

[Jochen Hub]

Gaurav Chopra wrote:


Hi

I get the following error when using mdrun for a protein in solution. 
I have checked the structure and everything looks fine to me. Could 
you suggested anything else I could do. 


How did you energy minimze your structure? What was the output of mdrun 
during energy minization, especially the last line with Fmax, Epot etc.?


I should look like this:

Step=   48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, 
atom= 78754
Step=   49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, 
atom= 13032
Step=   50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, 
atom= 13032


Jochen

--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de



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Re: [gmx-users] LINCS Warning using mdrun

[Steffen Wolf]

Gaurav Chopra wrote:

Hi

I get the following error when using mdrun for a protein in solution. 
I have checked the structure and everything looks fine to me. Could 
you suggested anything else I could do.


Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   898899   41.60.1015   0.0997  0.1010
   898900   38.10.1038   0.0984  0.1010
starting mdrun 'HEADER Output set 125 with rmsf= .982 of 
1nkd.cl_nH_tir.pdb in water'

10 steps,200.0 ps.


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:

Thanks
gaurav
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Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And 
have you run a minimization before starting the simulation?

hear from you soon
Steffen

--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany

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Re: [gmx-users] Range Checking Error

[David van der Spoel]

Gaurav Chopra wrote:

Gaurav Chopra wrote:

/ Hi
/>/ 
/>/ I am doing a steepest descent for the initial mdrun for a peptide and it 
/>/ gives me the following error. Please advice.
/>/ 
/>/ Thanks

/>/ Gaurav
/>/ ---
/>/ 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.
/Please follow the advice in the above two sentences. Check your structure.

I did the energy minimization by increasing the number of steps using steepest 
descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun 
but I got the following in my log file

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: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


Then with this when I do position restrained md, using -DPOSRES in mdp file for 
grompp and md integrator and then mdrun for position restrained
I get the following

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00
bonds that rotated more than 30 degrees:


turn off the constraints



also segmentation fault.

Is there a different method to do energy minimization better as suggested in 
the range check error warning.

Thanks
Gaurav



/ 

/>/ Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
/>/ Please report this to the mailing list (gmx-users at gromacs.org 
)
/>/ ---
/>/ 
/>/ ___

/>/ gmx-users mailing listgmx-users at gromacs.org 

/>/ http://www.gromacs.org/mailman/listinfo/gmx-users
/>/ Please don't post (un)subscribe requests to the list. Use the www 
/>/ interface or send it to gmx-users-request at gromacs.org. 

/>/ Can't post? Read http://www.gromacs.org/mailing_lists/users.php
/

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
spoel at xray.bmc.uu.se    
spoel at gromacs.org    
http://folding.bmc.uu.se





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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Range Checking Error

[Gaurav Chopra]

/ />/ 
/>/ />/ 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.
/>/ /Please follow the advice in the above two sentences. Check your structure.
/>/ 
/>/ I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE

/>/ and steep using -DFLEXIBLE in my mdp file and I was able to compute using 
mdrun but I got the following in my log file
/>/ 
/>/ 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: 24594
/>/ Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
/>/ Removing pbc first time
/>/ Done rmpbc
/>/ Steepest Descents:
/>/Tolerance (Fmax)   =  1.0e+01
/>/Number of steps=1
/>/ Grid: 10 x 10 x 20 cells
/>/ Configuring nonbonded kernels...
/>/ Testing AMD 3DNow support... not present.
/>/ Testing ia32 SSE support... present.
/>/ 
/>/ 
/>/ Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained

/>/ I get the following
/>/ 
/>/ Step 0, time 0 (ps)  LINCS WARNING

/>/ relative constraint deviation after LINCS:
/>/ max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00
/>/ bonds that rotated more than 30 degrees:
/
turn off the constraints






Hi David

I did turn off the constraints and also made the starting structure 
unconstarined in the mdp file. The mdrun for position restrained gives 
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the 
earlier mail which has to be reviewed by the moderator of gmx list.


Thanks
Gaurav


---
Input Parameters:
  integrator   = md
  nsteps   = 1000
  init_step= 0
  ns_type  = Grid
  nstlist  = 10
  ndelta   = 2
  bDomDecomp   = FALSE
  decomp_dir   = 0
  nstcomm  = 1
  comm_mode= Linear
  nstcheckpoint= 1000
  nstlog   = 1
  nstxout  = 0
  nstvout  = 250
  nstfout  = 0
  nstenergy= 250
  nstxtcout= 250
  init_t   = 0
  delta_t  = 0.002
  xtcprec  = 1000
  nkx  = 42
  nky  = 42
  nkz  = 84
  pme_order= 4
  ewald_rtol   = 1e-05
  ewald_geometry   = 0
  epsilon_surface  = 0
  optimize_fft = FALSE
  ePBC = xyz
  bUncStart= TRUE
  bShakeSOR= FALSE
  etc  = Berendsen
  epc  = Berendsen
  epctype  = Isotropic
  tau_p= 20
  ref_p (3x3):
 ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}
 ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
 ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
  compress (3x3):
 compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
 compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
 compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}
  andersen_seed= 815131
  rlist= 1
  coulombtype  = PME
  rcoulomb_switch  = 0
  rcoulomb = 1
  vdwtype  = Cut-off
  rvdw_switch  = 0
  rvdw = 1
  epsilon_r= 1
  epsilon_rf   = 1
  tabext   = 1
  gb_algorithm = Still
  nstgbradii   = 1
  rgbradii = 2
  gb_saltconc  = 0
  implicit_solvent = No
  DispCorr = No
  fudgeQQ  = 0.5
  free_energy  = no
  init_lambda  = 0
  sc_alpha = 0
  sc_power = 1
  sc_sigma = 0.3
  delta_lambda = 0
  disre_weighting  = Conservative
  disre_mixed  = FALSE
  dr_fc= 1000
  dr_tau   = 0
  nstdisreout  = 100
  orires_fc= 0
  orires_tau   = 0
  nstorireout  = 100
  dihre-fc = 1000
  dihre-tau= 0
  nstdihreout  = 100
  em_stepsize  = 0.01
  em_tol   = 10
  niter= 20
  fc_stepsize  = 0
  nstcgsteep   = 1000
  nbfgscorr= 10
  ConstAlg = Lincs
  shake_tol

[gmx-users] Range Checking Error

[Gaurav Chopra]

 />/ 
> />/ 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.
> /Please follow the advice in the above two sentences. Check your structure.
> 
> I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
> and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
> 
> 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: 24594
> Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
> Removing pbc first time
> Done rmpbc
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+01
>Number of steps=1
> Grid: 10 x 10 x 20 cells
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
> 
> 
> Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
> I get the following
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
> bonds that rotated more than 30 degrees:

turn off the constraints

>

Hi David

I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.

Thanks
Gaurav


---
Input Parameters:
   integrator   = md
   nsteps   = 1000
   init_step    = 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   bDomDecomp   = FALSE
   decomp_dir   = 0
   nstcomm  = 1
   comm_mode    = Linear
   nstcheckpoint    = 1000
   nstlog   = 1
   nstxout  = 0
   nstvout  = 250
   nstfout  = 0
   nstenergy    = 250
   nstxtcout    = 250
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 42
   nky  = 42
   nkz  = 84
   pme_order    = 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bUncStart    = TRUE
   bShakeSOR    = FALSE
   etc  = Berendsen
   epc  = Berendsen
   epctype  = Isotropic
   tau_p    = 20
   ref_p (3x3):
  ref_p[    0]={ 1.0e+00,  0.0e+00,  0.0e+00}
  ref_p[    1]={ 0.0e+00,  1.0e+00,  0.0e+00}
  ref_p[    2]={ 0.0e+00,  0.0e+00,  1.0e+00}
   compress (3x3):
  compress[    0]={ 4.5e-05,  0.0e+00,  0.0e+00}
  compress[    1]={ 0.0e+00,  4.5e-05,  0.0e+00}
  compress[    2]={ 0.0e+00,  0.0e+00,  4.5e-05}
   andersen_seed    = 815131
   rlist    = 1
   coulombtype  = PME
   rcoulomb_switch  = 0
   rcoulomb = 1
   vdwtype  = Cut-off
   rvdw_switch  = 0
   rvdw = 1
   epsilon_r    = 1
   epsilon_rf   = 1
   tabext   = 1
   gb_algorithm = Still
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   implicit_solvent = No
   DispCorr = No
   fudgeQQ  = 0.5
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 1
   sc_sigma = 0.3
   delta_lambda = 0
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc    = 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc    = 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   dihre-tau    = 0
   nstdihreout  = 100
   em_stepsize  = 0.01
   em_tol   = 10
   niter    = 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr    = 10
   ConstAlg = Lincs
   shake_tol

[gmx-users] LINCS Warning using mdrun

[Gaurav Chopra]

Hi

I get the following error when using mdrun for a protein in solution. I 
have checked the structure and everything looks fine to me. Could you 
suggested anything else I could do.


Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   898899   41.60.1015   0.0997  0.1010
   898900   38.10.1038   0.0984  0.1010
starting mdrun 'HEADER Output set 125 with rmsf= .982 of 
1nkd.cl_nH_tir.pdb in water'

10 steps,200.0 ps.


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:

Thanks
gaurav
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Re: [gmx-users] How 2 remove these warnings

[Yang Ye]

Check the line as specified in the warning. And translate the atom 
number to its atom type. Check such combination in the [dihedral] 
section in the ffX-nb.itp  whether there is such combination. I 
suspect that there is some mis-naming by pdb2gmx. Check the total charge 
of the molecule as well, it shall be a integer.


Yang Ye

Richa taimni wrote:

Hi,
I am getting these two warnings while doing the
pdb2gmx steps.Please give some suggestions on this
problem.



WARNING 1 [file "AFA.top", line 350]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 2 [file "AFA.top", line 455]:
  No default Ryckaert-Bell. types, using zeroes
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 1480
processing coordinates...
double-checking input for internal consistency

Regards,
Richa


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[gmx-users] How 2 remove these warnings

[Richa taimni]

Hi,
I am getting these two warnings while doing the
pdb2gmx steps.Please give some suggestions on this
problem.



WARNING 1 [file "AFA.top", line 350]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 2 [file "AFA.top", line 455]:
  No default Ryckaert-Bell. types, using zeroes
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 1480
processing coordinates...
double-checking input for internal consistency

Regards,
Richa


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[gmx-users] Re:g_clustsize problem

[Wang Zhun]

Hi, David,

Now I've got 12 clusters from my traj.trr and cluster members as well by 
g_cluster,
should I calculate the size of clusters by each #st/total #st, ie, for cluster 
12 38765/(1+8+21+141+...+38765)?

The g_clustsize "computes the size distributions of molecular/atomic clusters in
the gas phase. The output is given in the form of a XPM file. The total
number of clusters is written to a XVG file."(taken from help file).Is it not 
suitable to use g_clustsize command for my peptide in water solution ?

Thanks.

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[gmx-users] Range Checking error

[Gaurav Chopra]

Gaurav Chopra wrote:

/ Hi
/>/ 
/>/ I am doing a steepest descent for the initial mdrun for a peptide and it 
/>/ gives me the following error. Please advice.
/>/ 
/>/ Thanks

/>/ Gaurav
/>/ ---
/>/ 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.
/Please follow the advice in the above two sentences. Check your structure.

I did the energy minimization by increasing the number of steps using steepest 
descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun 
but I got the following in my log file

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: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
  Tolerance (Fmax)   =  1.0e+01
  Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


Then with this when I do position restrained md, using -DPOSRES in mdp file for 
grompp and md integrator and then mdrun for position restrained
I get the following

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00
bonds that rotated more than 30 degrees:

also segmentation fault.

Is there a different method to do energy minimization better as suggested in 
the range check error warning.

Thanks
Gaurav



/ 

/>/ Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
/>/ Please report this to the mailing list (gmx-users at gromacs.org 
)
/>/ ---
/>/ 
/>/ ___

/>/ gmx-users mailing listgmx-users at gromacs.org 

/>/ http://www.gromacs.org/mailman/listinfo/gmx-users
/>/ Please don't post (un)subscribe requests to the list. Use the www 
/>/ interface or send it to gmx-users-request at gromacs.org. 

/>/ Can't post? Read http://www.gromacs.org/mailing_lists/users.php
/

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
spoel at xray.bmc.uu.se    
spoel at gromacs.org    
http://folding.bmc.uu.se


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[gmx-users] Range Checking Error

[Gaurav Chopra]

Gaurav Chopra wrote:
> Hi
> 
> I am doing a steepest descent for the initial mdrun for a peptide and it 
> gives me the following error. Please advice.
> 
> Thanks
> Gaurav
> ---
> 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.
Please follow the advice in the above two sentences. Check your structure.

I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file

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: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
I get the following

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
bonds that rotated more than 30 degrees:

also segmentation fault.

Is there a different method to do energy minimization better as suggested in the range check error warning.

Thanks
Gaurav



> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> ---
> 
> ___
> gmx-users mailing listgmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
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-- 
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se



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[gmx-users] Parameters for OPLS

[Kobi]

Hello,

I'm equilibrating a Barnase/Barstar complex using OLPS Force Field, but 
I'm not sure which parameters I should use for PME. at the moment I'm 
using the following parameters:

coulombtype = PME
fourierspacing = 0.12
pme_order = 4
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0

Temperature Coupling ist turne on (berendsen) and Pressure Coupling is 
turend off. The size of the box is  4x5.8x10 nm.

thanks 
Kobi

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