[gmx-users] minimum image violation

[Kavyashree M]

Dear users,

I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only in the case of covalent dimer I was getting severe
minimum image violation ie. out of 50001 data points,
282 are <= 1.4nm
280 are < 1.4nm
144 are < 1.3nm
79 are < 1.2nm
28 are < 1.1nm
4 < 1.0nm

I agree that this is quite wrong but I wanted to know whether
any useful information can be gathered out of this simulation?

In another data while calculating the energy terms it gives
nan (not a number error) for rmsd alone eg -
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature 300  9e-05   -nan -0.000501989  (K)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure0.99914  0.027   -nan  0.0174391  (bar)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Volume  517.755 0.0094   -nan   0.010871  (nm^3)

Initially i though some data points are missing but later
gmxcheck gives that all the data points are present.
now what could be the error?

I had asked this question before and was instructed to check the
trajectory. I checked the rmsd rmsf of this with the other proteins
it similar but one of the segment has high rmsf compared to the other
proteins.

Thanking you
With regards
M. Kavyashree
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[gmx-users] Problem in followin MARTINI tutorial

[Naba]

Dear Users/Developers

I am trying to set a coarse-grained MD for the same protein (1UBQ.pdb)
therein the MARTINI tutorial (
http://md.chem.rug.nl/cgmartini/index.php/tutorial).
After the solvation by water-1bar-303K.gro I tried to minimize the system
but it gives the following weired results.

grompp gives the following output:

checking input for internal consistency...
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are:76Protein residues
There are:  5199  Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Making dummy/rest group for T-Coupling containing 5362 elements
Making dummy/rest group for Acceleration containing 5362 elements
Making dummy/rest group for Freeze containing 5362 elements
Making dummy/rest group for Energy Mon. containing 5362 elements
Making dummy/rest group for VCM containing 5362 elements
Number of degrees of freedom in T-Coupling group rest is 16053.00
Making dummy/rest group for User1 containing 5362 elements
Making dummy/rest group for User2 containing 5362 elements
Making dummy/rest group for XTC containing 5362 elements
Making dummy/rest group for Or. Res. Fit containing 5362 elements
Making dummy/rest group for QMMM containing 5362 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
This run will generate roughly 2 Mb of data
writing run input file...

But mdrun gives the following output:

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps= 5000
Step=   14, Dmax= 1.2e-06 nm, Epot=  3.55783e+18 Fmax= inf, atom=
294
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

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)

writing lowest energy coordinates.

Back Off! I just backed up solvated.gro to ./#solvated.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy  =  3.5578291e+18
Maximum force =inf on atom 294
Norm of force =  1.0627526e+19

Maximum force is equal to infinity and hence I am afraid to proceed further.
Can someone help me out?


Thanks in advance.

Nabajyoti Goswami

Senior Research Fellow
Bioinformatics Center, Sri Venkateswara College
University of Delhi South Campus
Benito Juarez Road, Dhaula Kuan
New Delhi 110021
India
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[gmx-users] convergence

[Gavin Melaugh]

Hi all

I have generated a PMF curve over 15 ns. Does g_wham have a facility
whereby I can calculate the PMF over say 7 ns, to check for convergence.
There doesn't seem to be anything in the manual.

Many thanks

Gavin
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[gmx-users] Re: convergence

[Gavin Melaugh]

Please ignore my last question, I have found the answer using the g_wham
-h option

Cheers

Gavin

Gavin Melaugh wrote:
> Hi all
>
> I have generated a PMF curve over 15 ns. Does g_wham have a facility
> whereby I can calculate the PMF over say 7 ns, to check for convergence.
> There doesn't seem to be anything in the manual.
>
> Many thanks
>
> Gavin
>
>   

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Re: [gmx-users] Problem in followin MARTINI tutorial

[XAvier Periole]

Well, there must be some thing some where that you did the wrong way :))

You should try again from the start and may be try to post on the  
Martini website forum

www.cgmartini.nl

XAvier

On Jun 20, 2011, at 9:41 AM, Naba wrote:


Dear Users/Developers

I am trying to set a coarse-grained MD for the same protein  
(1UBQ.pdb) therein the MARTINI tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial 
).
After the solvation by water-1bar-303K.gro I tried to minimize the  
system but it gives the following weired results.


grompp gives the following output:

checking input for internal consistency...
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are:76Protein residues
There are:  5199  Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and  
splitting into groups...

Making dummy/rest group for T-Coupling containing 5362 elements
Making dummy/rest group for Acceleration containing 5362 elements
Making dummy/rest group for Freeze containing 5362 elements
Making dummy/rest group for Energy Mon. containing 5362 elements
Making dummy/rest group for VCM containing 5362 elements
Number of degrees of freedom in T-Coupling group rest is 16053.00
Making dummy/rest group for User1 containing 5362 elements
Making dummy/rest group for User2 containing 5362 elements
Making dummy/rest group for XTC containing 5362 elements
Making dummy/rest group for Or. Res. Fit containing 5362 elements
Making dummy/rest group for QMMM containing 5362 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
This run will generate roughly 2 Mb of data
writing run input file...

But mdrun gives the following output:

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps= 5000
Step=   14, Dmax= 1.2e-06 nm, Epot=  3.55783e+18 Fmax= inf,  
atom= 294

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

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)

writing lowest energy coordinates.

Back Off! I just backed up solvated.gro to ./#solvated.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy  =  3.5578291e+18
Maximum force =inf on atom 294
Norm of force =  1.0627526e+19

Maximum force is equal to infinity and hence I am afraid to proceed  
further. Can someone help me out?



Thanks in advance.

Nabajyoti Goswami

Senior Research Fellow
Bioinformatics Center, Sri Venkateswara College
University of Delhi South Campus
Benito Juarez Road, Dhaula Kuan
New Delhi 110021
India

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[gmx-users] Generation of configurations for Umbrella Sampling

[Rebeca García Fandiño]

Hello,
I am trying to obtain the PMF from Umbrella Sampling of the process of 
separating two monomers of a dimer.
I am following the tutorial 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
and I have a doubt:
In this tutorial the generation of configurations is done using a .mdp file for 
pulling one chain from another, but is it possible to generate the 
configurations for Umbrella Sampling "by hand", I mean, changing the z 
coordinate of the monomer I want to move, then solvating and then minimizing 
these configurations? Is there any problem with this protocol for the obtaining 
of the configurations?
Thanks a lot for your help.
Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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[gmx-users] radius of gyration - compactness

[shahab shariati]

Dear all

I am studying md simulation of free protein and protein-ligand and
protein-dna complex.

In my simulation systems, the average of radius of gyration in free protein
is 2.31 and for protein in complex is 2.58.

I know the radius of gyration is measurement of compactness of the protein
as
smaller radius of gyration indicates protein is more compact,.

I encountered antithesis in two following paper:

1- The role of flexibility and hydration on the sequence-specific DNA
recognition by the Tn916 integrase protein: a molecular dynamics analysis.
J. Mol. Recognit. 2004; 17: 120–131.

[ Furthermore, INT–DBD appears less compact in the complex, as far as the
radius of gyration increases and more molecular surface is exposed to the
solvent (Table 1). ]

2- Molecular dynamics analysis of the engrailed homeodomain–DNA recognition.
Journal of Structural Biology 155 (2006) 426–437.

[ Furthermore, according to radiuses of gyration of two proteins in the two
systems, the protein in the complex is more
compact than the free protein, this is consistent with the result of
structure stability comparing. It means that less
molecular surface of homeodomain protein in the protein– DNA complex is
exposed to the solvent.]

please guide me about that.
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Re: [gmx-users] radius of gyration - compactness

[Tsjerk Wassenaar]

Hey Shahab,

What's the contradiction?

> [ Furthermore, INT–DBD appears less compact in the complex, as far as the
> radius of gyration increases and more molecular surface is exposed to the
> solvent (Table 1). ]

larger radius of gyration, less compact, more surface

> [ Furthermore, according to radiuses of gyration of two proteins in the two
> systems, the protein in the complex is more
> compact than the free protein, this is consistent with the result of
> structure stability comparing. It means that less
> molecular surface of homeodomain protein in the protein– DNA complex is
> exposed to the solvent.]

(smaller radius of gyration; not stated explicitly), more compact, less surface.

Seems consistent to me...

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] error bars g_wham

[Gavin Melaugh]

Hi all

I have read the manual and the recent JCTC paper on g_wham, and I was
wondering how to actually get the error bars on the profile.xvg file
outputted from g_wham.

Many Thanks

Gavin
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[gmx-users] adius of gyration - compactness

[shahab shariati]

Dear Tsjerk

thanks for your reply.

in paper 1 :

larger radius of gyration, less compact, more surface

in paper 2:
(smaller radius of gyration; not stated explicitly), more compact, less surface.

in paper 3:

[Journal of Structural Biology 156 (2006) 537–545]

Overall, the GBD appears a little more compact in the complex, as far
as the radius
of gyration decrease and less molecular surface is exposed to the solvent.

all of above is true.

I want to know exactly how do radius of gyration of protein from free
state to complex state change .
Rg increased od decreased?

What's the contradiction?

contradiction is in this that in paper 1 Rg increased and in paper 2
and 3 decreased.

I want to know my data [ In my simulation systems, the average of
radius of gyration in free protein
is 2.31 and for protein in complex is 2.58.] is true?
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Re: [gmx-users] adius of gyration - compactness

[Tsjerk Wassenaar]

Hi Shahab,

> I want to know exactly how do radius of gyration of protein from free state
> to complex state change .
> Rg increased od decreased?

That depends on the protein. Some will, e.g., close or fold upon
binding, while others may open up, or unfold.

> I want to know my data [ In my simulation systems, the average of radius of
> gyration in free protein
> is 2.31 and for protein in complex is 2.58.] is true?

It's true, because you found it. Whether it correctly reflects the
state of the system you're after depends on the quality of your model,
the time scale simulated and the tims scale of conformational changes
involved in (un)binding. There's no rule of thumb.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] radius of gyration - compactness - accessible surface area

[shahab shariati]

Dear Tsjerk

thanks for your attention.

 larger radius of gyration, more surface. and smaller radius of
gyration, less surface.

I want to obtain solvent accessible surface area using g_sas.

g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.

I will obtain three output files containing: area.xvg, resarea.xvg and
atomarea.xvg

If I want to obtain average of ASA  to compare with Rg (I want to know
in my system, with increase of Rg, how do ASA
change?), which of above output files are suitable for this aim?


best regards
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Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

[Mark Abraham]

On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:

I also checked the output of the minimization:

Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.81875038188621e+04
Maximum force =  3.20769543152855e+02 on atom 331
Norm of force =  2.04356801849931e+01

I assume the structure is not relaxed enough to start a simulation. 
How can I get it minimize further? I increased the step size up to 0.1 
ps, i still get the same result.


The minimization is probably OK, but a period of equilibration at a 
short time step will probably help smooth the process out. Simulations 
in implicit solvent have few explicit degrees of freedom compared to 
explicit solvent, and might be rather more susceptible to equilibration 
issues if the generated velocities are randomly not-quite-good-enough.


Mark


Thanks,
Nihal

On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz 
mailto:enihalkork...@gmail.com>> wrote:


Dear all,

I am trying to simulate a GB simulation of a 112 amino acid long
protein. I keep getting these errors,

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010
 79 80   90.00.1057   1.0667  0.1090
 79 81   90.01.3066  47.9342  0.1090
 85 86   90.00.1084   0.1758  0.1090
 85 87   90.01.0654   0.1668  0.1090
 88 89   90.00.1097   0.6994  0.1090
 88 90   90.00.1125   0.1097  0.1090
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010


I am copying my mdp parameters below, I'd appreciate any
suggestions to fix that.

integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 250
simulation_part  = 1
init_step= 1

nstxout  = 5000
nstvout  = 5000
nstenergy= 500
nstxtcout= 500
nstlog   = 500

xtc_grps = System
energygrps   = System
comm_mode= Linear
; neighbor searching and vdw/pme setting up
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 2.0

implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc  = 0.15
rgbradii = 2.0

coulombtype  = Cut-off
fourierspacing   = 0.1
pme_order= 6
rcoulomb = 2.0

vdwtype  = Cut-off
rvdw_switch  = 1.0
rvdw = 2.0

; cpt control
tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; velocity & temperature control
gen_vel  = yes
gen_temp = 300.0
annealing= no
constraints  = hbonds
constraint_algorithm = lincs
morse= no


Thanks,
-- 
Elif Nihal Korkmaz


Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 
Email: kork...@wisc.edu 





--
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 
Email: kork...@wisc.edu 




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[gmx-users] Fwd: Parallellization problem

[Nuria Alegret]

 Good afternoon,

I'm using GROMACS version 4.0.5. My simulation system is a double 
stranded DNA (51 nucleotides) in a water (TIPI3P type) box, defined as 
0.9 A from the DNA, with 100 Na ions to neutralize the system. The 
sequencial commands used were:


1) pdb2gmx -f dsDNA.pdb -p dsDNA.top -o dsDNA.gro -ffamber99

2) editconf -f dsDNA.gro -o box.gro -d 0.9

3) genbox -cp box.gro -cs ffamber_tip3p.gro -o water.gro -p dsDNA.top

4) grompp -f em.mdp -c water.gro -p dsDNA.top -o Premin.tpr

5) genion -s Premin.tpr -o water-ions.gro -np 100

6) grompp -f em.mdp -c water-ions.gro -p dsDNA.top -o minIons.tpr

7) MINIMIZATION:  mdrun -v -s minIons.tpr -o minIons_traj.trr -x 
minIons_traj.xtc -c minIons_final.gro -e minIons_ener.edr



The problem appears when I try to minimize the system. When I try to 
parallellize the calculation, the calculation returns with an error 
message as follows:


/Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the 
given box and a minimum cell size of 38.1122 nm

Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition/

According to your web page, this error appears when a very small system 
is too small to run parallellized. But my system is extremelly big!! In 
previous calcs I could parallellize smaller systems, even with just 8 
nucleotides.

I attach you the error file and the log file, as well as the mdp.
I would be gratefull with any help. Thanks in advance,



Núria Alegret
University Rovira i Virgili - Tarragona (Spain)


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 :-)  G  R  O  M  A  C  S  (-:

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  Gromacs Runs On Most of All Computer Systems

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  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
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 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

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Option Filename  Type Description

  -s   minIons2.tpr  InputRun input file: tpr tpb tpa
  -o minIons_traj2.trr  Output   Full precision trajectory: trr trj cpt
  -x minIons_traj2.xtc  Output, Opt! Compressed trajectory (portable xdr
   format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -c minIons_final2.gro  Output   Structure file: gro g96 pdb
  -e minIons_ener2.edr  Output   Energy file: edr ene
  -g md.log  Output   Log file
-dgdl  dgdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-n

Re: [gmx-users] Fwd: Parallellization problem

[Matthew Zwier]

I've had bad luck with parallel minimizations, particularly for the
4.0 series of GROMACS.  Either domain decomposition fails or numeric
problems appear (SETTLE failures and the like), but disappear when run
serially.  Minimization tends to be low cost compared to equilibration
anyway, so my solution has simply been never to run a minimization in
parallel, even for my large systems.  They're still done in minutes or
hours, compared to the hours or days required for equilibration.

On Mon, Jun 20, 2011 at 11:41 AM, Nuria Alegret  wrote:
>
>  Good afternoon,
>
> I'm using GROMACS version 4.0.5. My simulation system is a double stranded
> DNA (51 nucleotides) in a water (TIPI3P type) box, defined as 0.9 A from the
> DNA, with 100 Na ions to neutralize the system. The sequencial commands used
> were:
>
> 1) pdb2gmx -f dsDNA.pdb -p dsDNA.top -o dsDNA.gro -ffamber99
>
> 2) editconf -f dsDNA.gro -o box.gro -d 0.9
>
> 3) genbox -cp box.gro -cs ffamber_tip3p.gro -o water.gro -p dsDNA.top
>
> 4) grompp -f em.mdp -c water.gro -p dsDNA.top -o Premin.tpr
>
> 5) genion -s Premin.tpr -o water-ions.gro -np 100
>
> 6) grompp -f em.mdp -c water-ions.gro -p dsDNA.top -o minIons.tpr
>
> 7) MINIMIZATION:  mdrun -v -s minIons.tpr -o minIons_traj.trr -x
> minIons_traj.xtc -c minIons_final.gro -e minIons_ener.edr
>
>
> The problem appears when I try to minimize the system. When I try to
> parallellize the calculation, the calculation returns with an error message
> as follows:
>
> Fatal error:
> There is no domain decomposition for 8 nodes that is compatible with the
> given box and a minimum cell size of 38.1122 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
>
> According to your web page, this error appears when a very small system is
> too small to run parallellized. But my system is extremelly big!! In
> previous calcs I could parallellize smaller systems, even with just 8
> nucleotides.
> I attach you the error file and the log file, as well as the mdp.
> I would be gratefull with any help. Thanks in advance,
>
>
>
> Núria Alegret
> University Rovira i Virgili - Tarragona (Spain)
>
>
>
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Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

[E. Nihal Korkmaz]

What would you suggest as a short time step? I was using 0.002 ps. And just
to make sure, would 5 ns of equilibration be enough for a ~110 amino acid
long protein?

Thanks,
Nihal

On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham wrote:

> **
> On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
>
> I also checked the output of the minimization:
>
> Steepest Descents converged to machine precision in 402 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -1.81875038188621e+04
> Maximum force =  3.20769543152855e+02 on atom 331
> Norm of force =  2.04356801849931e+01
>
> I assume the structure is not relaxed enough to start a simulation. How can
> I get it minimize further? I increased the step size up to 0.1 ps, i still
> get the same result.
>
>
> The minimization is probably OK, but a period of equilibration at a short
> time step will probably help smooth the process out. Simulations in implicit
> solvent have few explicit degrees of freedom compared to explicit solvent,
> and might be rather more susceptible to equilibration issues if the
> generated velocities are randomly not-quite-good-enough.
>
> Mark
>
>
> Thanks,
> Nihal
>
> On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz <
> enihalkork...@gmail.com> wrote:
>
>> Dear all,
>>
>> I am trying to simulate a GB simulation of a 112 amino acid long protein.
>> I keep getting these errors,
>>
>> Step 27718, time 55.436 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 33.319842, max 438.763717 (between atoms 79 and 81)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 27718, time 55.436 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.058237, max 1.390675 (between atoms 91 and 93)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>  91 92   50.20.1016   0.1065  0.1010
>>  91 93   90.00.1002   0.2415  0.1010
>>  91 94   70.20.1025   0.1066  0.1010
>>  79 80   90.00.1057   1.0667  0.1090
>>  79 81   90.01.3066  47.9342  0.1090
>>  85 86   90.00.1084   0.1758  0.1090
>>  85 87   90.01.0654   0.1668  0.1090
>>  88 89   90.00.1097   0.6994  0.1090
>>  88 90   90.00.1125   0.1097  0.1090
>>  91 92   50.20.1016   0.1065  0.1010
>>  91 93   90.00.1002   0.2415  0.1010
>>  91 94   70.20.1025   0.1066  0.1010
>>
>>
>> I am copying my mdp parameters below, I'd appreciate any suggestions to
>> fix that.
>>
>> integrator   = sd
>> tinit= 0
>> dt   = 0.002
>> nsteps   = 250
>> simulation_part  = 1
>> init_step= 1
>>
>> nstxout  = 5000
>> nstvout  = 5000
>> nstenergy= 500
>> nstxtcout= 500
>> nstlog   = 500
>>
>> xtc_grps = System
>> energygrps   = System
>> comm_mode= Linear
>> ; neighbor searching and vdw/pme setting up
>> nstlist  = 10
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 2.0
>>
>> implicit_solvent = GBSA
>> gb_algorithm = OBC
>> gb_saltconc  = 0.15
>> rgbradii = 2.0
>>
>> coulombtype  = Cut-off
>> fourierspacing   = 0.1
>> pme_order= 6
>> rcoulomb = 2.0
>>
>> vdwtype  = Cut-off
>> rvdw_switch  = 1.0
>> rvdw = 2.0
>>
>> ; cpt control
>> tcoupl   = V-rescale
>> tc-grps  = System
>> tau_t= 0.1
>> ref_t= 300.0
>>
>> Pcoupl   = Berendsen
>> pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>>
>> ; velocity & temperature control
>> gen_vel  = yes
>> gen_temp = 300.0
>> annealing= no
>> constraints  = hbonds
>> constraint_algorithm = lincs
>> morse= no
>>
>>
>> Thanks,
>> --
>> Elif Nihal Korkmaz
>>
>> Research Assistant
>> University of Wisconsin - Biophysics
>> Member of Qiang Cui & Thomas Record Labs
>> 1101 University Ave, Rm. 8359
>> Madison, WI 53706
>> Phone:  608-265-3644
>> Email:   kork...@wisc.edu
>>
>>
>>
>
>
> --
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email:   kork...@wisc.edu
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archiv

Re: Re: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field

[udaya kiran marelli]

Dear Mark Abraham,

Thank you for your support.  However, I have edited the N-terminus in -hdb
file so as too include a HN atom for the specific residue and it worked.

regards,
Uday..

On Fri, Jun 17, 2011 at 10:29 PM,  wrote:

> Send gmx-users mailing list submissions to
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> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. cyclic peptide on GROMACS compatoble with Charmm  (all-atom)
>  force field (udaya kiran marelli)
>   2. Re: gmx4.5.4 genion problem: No line with moleculetype'SOL'
>  found (Ye Yang)
>   3. gmx4.5.4 genion problem: No line with moleculetype'SOL'
>  found (chris.ne...@utoronto.ca)
>   4. Re: cyclic peptide on GROMACS compatoble with Charmm
>  (all-atom) force field (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Fri, 17 Jun 2011 17:13:54 +0200
> From: udaya kiran marelli 
> Subject: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm
>(all-atom) force field
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
>  Dear GROMACS users,
>
> I am trying to construct a cyclic hexa peptide containing all Ala residues.
>  During pdb2gmx conversion using the command(pdb2gmx -ff charmm27 -ignh
> -f TESTALA.pdb -o TESTALA.gro -ter)  it gave the following error while I am
> demanding the program to give uncharged termini (option :  None)
>
> WARNING: atom HN is missing in residue ALA 1 in the pdb file
>You might need to add atom HN to the hydrogen database of residue
> ALA
>in the file ff???.hdb (see the manual)
>
>
> ---
> Program pdb2gmx, VERSION 4.0.5
> Source code file: pdb2top.c, line: 704
>
> Fatal error:
> There were 1 missing atoms in molecule Protein, if you want to use this
> incomplete topology anyhow, use the option -missing
>
> In the .hdb file the atom HN is defined already.  The error is that it is
> removing the #HN# atom from the Ala 1 residue at the cyclization point.
>
> Could you suggest me in getting rid off the problem.
>
>
> yours sincerely
> Uday.
>
> Marelli Udaya Kiran
> C/o.  Professor Dr. Horst Kessler
> Institute for Advanced Study
> Department Chemie
> Technische Universität München
> Lichtenbergstrasse 4
> D-85747 Garching, Germany
>
> Tel.: +49-(0)89-289-13760
> Fax: +49-(0)89-289-13210
> email: kiran.ud...@tum.de
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110617/2685133e/attachment-0001.html
>
> --
>
> Message: 2
> Date: Fri, 17 Jun 2011 13:06:44 -0400
> From: Ye Yang 
> Subject: Re: [gmx-users] gmx4.5.4 genion problem: No line with
>moleculetype'SOL' found
> To: jalem...@vt.edu, Discussion list for GROMACS users
>
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you for your suggestions.
> I have checked the topology file with vim, and it looks pefectly, also, the
> only problem happens when I use genion. One thing that might be possible is
> that I use the double precision version of gromacs, because when I solve it
> in water, the written of topology file looks weired(like I showed).
> What do you mean by work-around? You mean just manually change some water
> molecules in topology file and coordinate file into ions? Will the program
> recognize something like CL, NA? Or can I just add ions to the system and
> solve it in water?
>
> Thank you very much
>
> Best
> Wishes
>
> Ye
>
> 2011/6/16 Justin A. Lemkul 
>
> >
> >
> > Ye Yang wrote:
> >
> >> Hi, everyone:
> >>  I am a new user of Gromacs, and I am running through the tutorial.
> >> When I am trying to run the ligand-receptor binding tutorial from
> >>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
> >> I met some trouble in adding ion.
> >> Each time when I use genion, it shows:
> >>
> >> Will try to add 0 NA ions and 6 CL ions.
> >> Select a continuous group of solvent molecules
> >> Group 0 ( System) has 33046 elements
> >> Group 1 (Protein) has  1693 elements
> >> Group 2 (  Protein-H) has  1301 elements
> >> Group 3 (C-alpha) has   163 elements
> >> Group 4 (   Backbone) has   489 elements
> >> Group 5 (  MainChain) has   653 elements
> >> Group 6 (   MainChain+Cb) has   805 elements
> >> Group 7 (MainChain+H) has   815 elements
> 

[gmx-users] NVT equilibration of DMSO solvent (Charmm all-atom force field)

[udaya kiran marelli]

Dear GROMACS users,

I have generated a 4*4*4 octahedral DMSO box containing 64 molecules (Charmm
all-atom force field) which need to be NVT equilibrated in order to pass it
for usage in genbox.  Could one of you provide info on how to do the NVT and
periodic boundary equilibration to remove the residual ordering of the
solvent?

Thanking you in advance

yours sincerely,
Uday.
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[gmx-users] EM broke protein-lipid system

[Du Jiangfeng (BIOCH)]

Dear Gromacs Users,
It comes to me with million problems per day during I am using gromacs. :(
Maybe you are the right persons i should ask about coarse grained protein-lipid 
simulation. Right now I have a system with a bilayer (DOPCs) and a protein 
(Histone). After EM simulation, it worked quite well Then, this system was 
filled with water and was performed by EM again. Then it was scattered 
severely. Though I tried lipid constraint and many other methods, the problem 
is still here
Any suggestions?
Thank you guys in advance,



Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands--
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Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

[Mark Abraham]

On 21/06/2011 2:10 AM, E. Nihal Korkmaz wrote:

What would you suggest as a short time step? I was using 0.002 ps.


I'd suggest starting with maybe 100ps of 0.0005 ps time steps, but 
that's probably overkill.


And just to make sure, would 5 ns of equilibration be enough for a 
~110 amino acid long protein?


I guess so. It's cheap.

Mark


Thanks,
Nihal

On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham > wrote:


On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:

I also checked the output of the minimization:

Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.81875038188621e+04
Maximum force =  3.20769543152855e+02 on atom 331
Norm of force =  2.04356801849931e+01

I assume the structure is not relaxed enough to start a
simulation. How can I get it minimize further? I increased the
step size up to 0.1 ps, i still get the same result.


The minimization is probably OK, but a period of equilibration at
a short time step will probably help smooth the process out.
Simulations in implicit solvent have few explicit degrees of
freedom compared to explicit solvent, and might be rather more
susceptible to equilibration issues if the generated velocities
are randomly not-quite-good-enough.

Mark



Thanks,
Nihal

On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz
mailto:enihalkork...@gmail.com>> wrote:

Dear all,

I am trying to simulate a GB simulation of a 112 amino acid
long protein. I keep getting these errors,

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010
 79 80   90.00.1057   1.0667  0.1090
 79 81   90.01.3066  47.9342  0.1090
 85 86   90.00.1084   0.1758  0.1090
 85 87   90.01.0654   0.1668  0.1090
 88 89   90.00.1097   0.6994  0.1090
 88 90   90.00.1125   0.1097  0.1090
 91 92   50.20.1016   0.1065  0.1010
 91 93   90.00.1002   0.2415  0.1010
 91 94   70.20.1025   0.1066  0.1010


I am copying my mdp parameters below, I'd appreciate any
suggestions to fix that.

integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 250
simulation_part  = 1
init_step= 1

nstxout  = 5000
nstvout  = 5000
nstenergy= 500
nstxtcout= 500
nstlog   = 500

xtc_grps = System
energygrps   = System
comm_mode= Linear
; neighbor searching and vdw/pme setting up
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 2.0

implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc  = 0.15
rgbradii = 2.0

coulombtype  = Cut-off
fourierspacing   = 0.1
pme_order= 6
rcoulomb = 2.0

vdwtype  = Cut-off
rvdw_switch  = 1.0
rvdw = 2.0

; cpt control
tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; velocity & temperature control
gen_vel  = yes
gen_temp = 300.0
annealing= no
constraints  = hbonds
constraint_algorithm = lincs
morse= no


Thanks,
-- 
Elif Nihal Korkmaz

Re: [gmx-users] NVT equilibration of DMSO solvent (Charmm all-atom force field)

[Mark Abraham]

On 21/06/2011 2:44 AM, udaya kiran marelli wrote:

Dear GROMACS users,

I have generated a 4*4*4 octahedral DMSO box containing 64 molecules 
(Charmm all-atom force field) which need to be NVT equilibrated in 
order to pass it for usage in genbox.  Could one of you provide info 
on how to do the NVT and periodic boundary equilibration to remove the 
residual ordering of the solvent?


Most tutorials will cover the details of such stages well.

Mark
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Re: [gmx-users] EM broke protein-lipid system

[Mark Abraham]

On 21/06/2011 2:46 AM, Du Jiangfeng (BIOCH) wrote:

Dear Gromacs Users,
It comes to me with million problems per day during I am using gromacs. :(


Computational chemistry is rarely easy. The tasks are complex and 
demanding, even when the software is mature and the documentation well 
written... That said, you're tackling a difficult multi-phase system...



Maybe you are the right persons i should ask about coarse grained protein-lipid 
simulation. Right now I have a system with a bilayer (DOPCs) and a protein 
(Histone). After EM simulation, it worked quite well Then, this system was 
filled with water and was performed by EM again. Then it was scattered 
severely. Though I tried lipid constraint and many other methods, the problem 
is still here
Any suggestions?


I can only suggest that you find and follow suitable tutorial material, 
simplifying your system as much as you can, adding complexity in stages.


Mark
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[gmx-users] Re: doubt about your Umbrella Sampling tutorial

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Dear Justin,
my name is Rebeca and I am a postdoctoral student in Santiago de 
Compostela University. Sorry for disturbing you to your personal mail, I 
have tried to post to the Gromacs-list first, but I did not get any answer.


I was traveling and not paying much attention to messages across the list.  I 
will CC this reply to the list in the hopes that it is useful to others, as well.


I am trying to obtain the PMF from Umbrella Sampling of the process of 
separating two monomers of a dimer, following your tutorial, and I have 
a pair of doubts:


1)In this tutorial the generation of configurations is done using a .mdp 
file for pulling one chain from another, but is it possible to generate 
the configurations for Umbrella Sampling "by hand", I mean, changing the 
z coordinate of the monomer I want to move, then solvating and then 
minimizing these configurations? Is there any problem with this protocol 
for the obtaining of the configurations?




No problem at all.  The tutorial is but one possible method.

2) I have noticed that you use restraints in the md_umbrella.mdp for the 
fixed chain. Is that correct? I can understand the restraints in the 
pulling simulations for generate starting configurations, but once you 
have the configurations, is is necessary to restrain one part of the 
system?




Not usually.  The tutorial presents a special case.

Thanks a lot in advance for your help with this topic, and thank you 
very much also for publishing this interesting tutorial. There was 
nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I 
think it is more than wellcome for all Gromacs users!


Glad they're useful :)

-Justin


Best wishes,
Rebeca.

Dr. Rebeca García Fandiño
Department of Organic Chemistry and Center for Research in Biological 
Chemistry

and Molecular Materials
Santiago de Compostela University
E-15782 Santiago de Compostela (Spain)
e-mail: rebeca.garcia.fand...@usc.es
Phone: 34-981563100 ext 15760









--


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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Re: [gmx-users] minimum image violation

[Justin A. Lemkul]

Kavyashree M wrote:

Dear users,
 
I ran 100ns simulation for 4 proteins, 3 of them were

non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only in the case of covalent dimer I was getting severe
minimum image violation ie. out of 50001 data points,
282 are <= 1.4nm
280 are < 1.4nm
144 are < 1.3nm
79 are < 1.2nm
28 are < 1.1nm
4 < 1.0nm

I agree that this is quite wrong but I wanted to know whether
any useful information can be gathered out of this simulation?
 


Not likely.  Nearly 2% of the saved frames are unusable, indicating that 
potentially even more of the frames in the trajectory are useless, as well, and 
the dynamics that produced them are flawed.



In another data while calculating the energy terms it gives
nan (not a number error) for rmsd alone eg -
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature 300  9e-05   -nan -0.000501989  (K)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure0.99914  0.027   -nan  0.0174391  (bar)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Volume  517.755 0.0094   -nan   0.010871  (nm^3)
 
Initially i though some data points are missing but later

gmxcheck gives that all the data points are present.
now what could be the error?

I had asked this question before and was instructed to check the
trajectory. I checked the rmsd rmsf of this with the other proteins
it similar but one of the segment has high rmsf compared to the other
proteins.



My advice to you was to *watch* the trajectory to see where the PBC violations 
occurred, not run more analysis.  I doubt RMSF and RMSD will tell you anything 
useful.


No one's been able to diagnose the problem based on this (continually posted) 
information.  If it's a useless trajectory, why bother?


-Justin


Thanking you
With regards
M. Kavyashree





--


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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Re: [gmx-users] error bars g_wham

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi all

I have read the manual and the recent JCTC paper on g_wham, and I was
wondering how to actually get the error bars on the profile.xvg file
outputted from g_wham.


A suitable combination of g_wham -bs-method -nBootstrap, etc.  See g_wham -h.

-Justin

--


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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[gmx-users] NMR chemical shift restraints

[Thomas Evangelidis]

Dear GROMACS users,

I've read in the manual and in previous posts that NMR chemical shifts can
be computed from phi/psi angles. However, it was unclear whether the inverse
is possible with GROMACS, namely to use chemical shifts (1H, 13C, 15N) as
restraints (possibly as secondary structure restraints with a given
propensity) during MD simulations. I would be grateful if any experienced
member could clarify this for me.

thanks in advance,
Thomas




-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] NMR chemical shift restraints

[Mark Abraham]

On 21/06/2011 8:30 AM, Thomas Evangelidis wrote:

Dear GROMACS users,

I've read in the manual and in previous posts that NMR chemical shifts 
can be computed from phi/psi angles. However, it was unclear whether 
the inverse is possible with GROMACS, namely to use chemical shifts 
(1H, 13C, 15N) as restraints (possibly as secondary structure 
restraints with a given propensity) during MD simulations. I would be 
grateful if any experienced member could clarify this for me.



Various kinds of (time-averaged) restraints can be imposed (details in 
the manual), and NMR data can be the source for these. For details of 
the latter, I can only suggest searching the literature for publications 
that report how they derived such restraints.


Mark
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[gmx-users] Re: Increase in charge after adding the ligand

[bharat gupta]

Hi,

Initially while preparing the structure , -2 charge was there on the
protein. Next, after adding the ligand and executing grompp statement It
showing -9.9 charge. So I added 9 sodium ions. but still its showing +8
charge on the system. what shall I do in this case ??

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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[gmx-users] Re: Error during executing the protein ligand tutorial

[bharat gupta]

Hi,

In addition to my last mail, I am also getting another error during the
minimization step. I made the changes in em_real.mdp file for my sytem but
its showing the error that "ource code file: readir.c, line: 1316

Fatal error:
Group PTR not found in indexfile.
"

also the charge on the system now is 8  pls help

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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RE: [gmx-users] Re: Increase in charge after adding the ligand

[Dallas Warren]

You need to work out exactly why you have the mis-match, something is screwy.

Something that you are doing does not add up.

What is the charge on the ligand?  Appears to be -7.

Why when you add 9 Na+ do you then end up with a charge of +8?  Seems that you 
have actually added 17 sodiums from those numbers.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of bharat gupta
Sent: Tuesday, 21 June 2011 12:05 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Re: Increase in charge after adding the ligand

Hi,

Initially while preparing the structure , -2 charge was there on the protein. 
Next, after adding the ligand and executing grompp statement It showing -9.9 
charge. So I added 9 sodium ions. but still its showing +8 charge on the 
system. what shall I do in this case ??

--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com

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Re: [gmx-users] Re: Increase in charge after adding the ligand

[bharat gupta]

I checked the .gro file , in that only 9 NA are mentioned.. also during the
minimization step I am getting the following error:-

step 100: Water molecule starting at atom 85940 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  100, Dmax= 2.4e-01 nm, Epot= -4.86897e+06 Fmax= 2.60577e+06, atom=
85940
Step=  101, Dmax= 2.8e-01 nm, Epot= -4.88265e+06 Fmax= 1.03794e+05, atom=
3628

step 102: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  102, Dmax= 3.4e-01 nm, Epot=  7.97834e+06 Fmax= 1.57210e+09, atom=
3631
step 103: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  104, Dmax= 8.5e-02 nm, Epot= -4.90566e+06 Fmax= 2.85624e+05, atom=
3628
Step=  105, Dmax= 1.0e-01 nm, Epot= -4.91390e+06 Fmax= 1.97964e+05, atom=
3628

step 106: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  107, Dmax= 6.2e-02 nm, Epot= -4.92487e+06 Fmax= 6.32096e+04, atom=
362885
Step=  108, Dmax= 7.4e-02 nm, Epot= -4.95276e+06 Fmax= 4.18514e+04, atom=
3627
Step=  109, Dmax= 8.9e-02 nm, Epot= -4.98566e+06 Fmax= 1.91771e+05, atom=
3620
Step=  110, Dmax= 1.1e-01 nm, Epot= -5.00651e+06 Fmax= 1.56721e+05, atom=
3620
Step=  112, Dmax= 6.4e-02 nm, Epot= -5.01376e+06 Fmax= 1.25375e+05, atom=
3620
Step=  113, Dmax= 7.7e-02 nm, Epot= -5.02950e+06 Fmax= 5.35431e+04, atom=
3620
Step=  114, Dmax= 9.2e-02 nm, Epot= -5.04978e+06 Fmax= 2.03884e+05, atom=
3620
Step=  115, Dmax= 1.1e-01 nm, Epot= -5.07406e+06 Fmax= 6.55437e+04, atom=
3620
Step=  116, Dmax= 1.3e-01 nm, Epot= -5.10420e+06 Fmax= 4.48874e+05, atom=
3620
Step=  117, Dmax= 1.6e-01 nm, Epot= -5.11132e+06 Fmax= 1.89966e+05, atom=
3620

step 118: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  118, Dmax= 1.9e-01 nm, Epot= -5.12615e+06 Fmax= 2.25039e+05, atom=
3620

step 119: Water molecule starting at atom 252632 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 119: Water molecule starting at atom 212687 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=  119, Dmax= 2.3e-01 nm, Epot= -5.15014e+06 Fmax= 1.78972e+07, atom=
212687
Step=  120, Dmax= 2.7e-01 nm, Epot= -5.15139e+06 Fmax= 9.55607e+04, atom=
3620

step 121: Water molecule starting at atom 171371 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  122, Dmax= 1.6e-01 nm, Epot= -5.16214e+06 Fmax= 3.02686e+05, atom=
3620
Step=  123, Dmax= 2.0e-01 nm, Epot= -5.18637e+06 Fmax= 1.61921e+05, atom=
3620
Step=  124, Dmax= 2.4e-01 nm, Epot= -5.21873e+06 Fmax= 7.51816e+04, atom=
3620

step 125: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  125, Dmax= 2.8e-01 nm, Epot= -5.13297e+06 Fmax= 1.02333e+08, atom=
212927
step 126: Water molecule starting at atom 212927 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  126, Dmax= 1.4e-01 nm, Epot= -5.23551e+06 Fmax= 2.01165e+05, atom=
3620
Step=  127, Dmax= 1.7e-01 nm, Epot= -5.25949e+06 Fmax= 9.03334e+04, atom=
3620
Step=  129, Dmax= 1.0e-01 nm, Epot= -5.27727e+06 Fmax= 1.03222e+05, atom=
3620
Step=  130, Dmax= 1.2e-01 nm, Epot= -5.29146e+06 Fmax= 1.41302e+05, atom=
3630
Step=  132, Dmax= 7.4e-02 nm, Epot= -5.30238e+06 Fmax= 7.19601e+04, atom=
3630
Step=  133, Dmax= 8.8e-02 nm, Epot= -5.32013e+06 Fmax= 5.75864e+04, atom=
3630
Step=  134, Dmax= 1.1e-01 nm, Epot= -5.33172e+06 Fmax= 1.98591e+05, atom=
3622
Step=  135, Dmax= 1.3e-01 nm, Epot= -5.34273e+06 Fmax= 1.20478e+05, atom=
3622
Step=  136, Dmax= 1.5e-01 nm, Epot= -5.36395e+06 Fmax= 7.56979e+04, atom=
3620
Step=  138, Dmax= 9.2e-02 nm, Epot= -5.37722e+06 Fmax= 7.34765e+04, atom=
3622
Step=  139, Dmax= 1.1e-01 nm, Epot= -5.38280e+06 Fmax= 2.57798e+05, atom=
3622
Step=  140, Dmax= 1.3e-01 nm, Epot= -5.39328e+06 Fmax= 5.13241e+05, atom=
3622

step 141: Water molecule starting at atom 171395 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  142, Dmax= 7.9e-02 nm, Epot= -5.40360e+06 Fmax= 5.65055e+04, atom=
362295
Step=  14

RE: [gmx-users] Re: Increase in charge after adding the ligand

[Dallas Warren]

Go back through your procedure, repeating it again, step by step.  Take note of 
number of atoms, charges etc as you go.  And answer the other questions I put 
to you previously.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of bharat gupta
Sent: Tuesday, 21 June 2011 12:31 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: Increase in charge after adding the ligand

I checked the .gro file , in that only 9 NA are mentioned.. also during the 
minimization step I am getting the following error:-

step 100: Water molecule starting at atom 85940 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  100, Dmax= 2.4e-01 nm, Epot= -4.86897e+06 Fmax= 2.60577e+06, atom= 85940
Step=  101, Dmax= 2.8e-01 nm, Epot= -4.88265e+06 Fmax= 1.03794e+05, atom= 3628

step 102: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  102, Dmax= 3.4e-01 nm, Epot=  7.97834e+06 Fmax= 1.57210e+09, atom= 3631
step 103: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  104, Dmax= 8.5e-02 nm, Epot= -4.90566e+06 Fmax= 2.85624e+05, atom= 3628
Step=  105, Dmax= 1.0e-01 nm, Epot= -4.91390e+06 Fmax= 1.97964e+05, atom= 3628

step 106: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  107, Dmax= 6.2e-02 nm, Epot= -4.92487e+06 Fmax= 6.32096e+04, atom= 362885
Step=  108, Dmax= 7.4e-02 nm, Epot= -4.95276e+06 Fmax= 4.18514e+04, atom= 3627
Step=  109, Dmax= 8.9e-02 nm, Epot= -4.98566e+06 Fmax= 1.91771e+05, atom= 3620
Step=  110, Dmax= 1.1e-01 nm, Epot= -5.00651e+06 Fmax= 1.56721e+05, atom= 3620
Step=  112, Dmax= 6.4e-02 nm, Epot= -5.01376e+06 Fmax= 1.25375e+05, atom= 3620
Step=  113, Dmax= 7.7e-02 nm, Epot= -5.02950e+06 Fmax= 5.35431e+04, atom= 3620
Step=  114, Dmax= 9.2e-02 nm, Epot= -5.04978e+06 Fmax= 2.03884e+05, atom= 3620
Step=  115, Dmax= 1.1e-01 nm, Epot= -5.07406e+06 Fmax= 6.55437e+04, atom= 3620
Step=  116, Dmax= 1.3e-01 nm, Epot= -5.10420e+06 Fmax= 4.48874e+05, atom= 3620
Step=  117, Dmax= 1.6e-01 nm, Epot= -5.11132e+06 Fmax= 1.89966e+05, atom= 3620

step 118: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  118, Dmax= 1.9e-01 nm, Epot= -5.12615e+06 Fmax= 2.25039e+05, atom= 3620

step 119: Water molecule starting at atom 252632 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 119: Water molecule starting at atom 212687 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=  119, Dmax= 2.3e-01 nm, Epot= -5.15014e+06 Fmax= 1.78972e+07, atom= 212687
Step=  120, Dmax= 2.7e-01 nm, Epot= -5.15139e+06 Fmax= 9.55607e+04, atom= 3620

step 121: Water molecule starting at atom 171371 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  122, Dmax= 1.6e-01 nm, Epot= -5.16214e+06 Fmax= 3.02686e+05, atom= 3620
Step=  123, Dmax= 2.0e-01 nm, Epot= -5.18637e+06 Fmax= 1.61921e+05, atom= 3620
Step=  124, Dmax= 2.4e-01 nm, Epot= -5.21873e+06 Fmax= 7.51816e+04, atom= 3620

step 125: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  125, Dmax= 2.8e-01 nm, Epot= -5.13297e+06 Fmax= 1.02333e+08, atom= 212927
step 126: Water molecule starting at atom 212927 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  126, Dmax= 1.4e-01 nm, Epot= -5.23551e+06 Fmax= 2.01165e+05, atom= 3620
Step=  127, Dmax= 1.7e-01 nm, Epot= -5.25949e+06 Fmax= 9.03334e+04, atom= 3620
Step=  129, Dmax= 1.0e-01 nm, Epot= -5.27727e+06 Fmax= 1.03222e+05, atom= 3620
Step=  130, Dmax= 1.2e-01 nm, Epot= -5.29146e+06 Fmax= 1.41302e+05, atom= 3630
Step=  132, Dmax= 7.4e-02 nm, Epot= -5.30238e+06 Fmax= 7.19601e+04, atom= 3630
Step=  133, Dmax= 8.8e-02 nm, Epot= -5.32013e+06 Fmax= 5.75864e+04, atom= 3630
S

Re: [gmx-users] Re: Increase in charge after adding the ligand

[Mark Abraham]

On 21/06/2011 12:05 PM, bharat gupta wrote:

Hi,

Initially while preparing the structure , -2 charge was there on the 
protein. Next, after adding the ligand and executing grompp statement 
It showing -9.9 charge.


See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic, 
which may be relevant.


So I added 9 sodium ions. but still its showing +8 charge on the 
system. what shall I do in this case ??


-9.9 has been filtered through your head. We'd much rather see the 
output of your terminal, copied and pasted. There's no way that -9.9 
plus 9 sodium atoms gives +8. There must be a gap in your understanding 
somewhere, which is why we want to see actual input and output, not 
guesses and memories :-)


Mark
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[Justin A. Lemkul]

bharat gupta wrote:

Hi,

In addition to my last mail, I am also getting another error during the 
minimization step. I made the changes in em_real.mdp file for my sytem 
but its showing the error that "ource code file: readir.c, line: 1316


Fatal error:
Group PTR not found in indexfile.
"



I'm guessing you failed to follow step 5 here:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field


also the charge on the system now is 8  pls help


Take another look at the screen output regarding net charge before adding ions. 
 I suspect you're missing an exponent.  But I'd echo what Mark has said - 
always provide real output directly copied from the screen, or else we're left 
to our suspicions and guesses, which ends up wasting everyone's time.


-Justin

--


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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[gmx-users] radius of gyration - compactness - accessible surface area

[shahab shariati]

Dear Tsjerk

thanks for your attention.

 larger radius of gyration, more surface. and smaller radius of
gyration, less surface.

I want to obtain solvent accessible surface area using g_sas.

g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.

I will obtain three output files containing: area.xvg, resarea.xvg and
atomarea.xvg

If I want to obtain average of ASA  to compare with Rg (I want to know
in my system, with increase of Rg, how do ASA
change?), which of above output files are suitable for this aim?
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[bharat gupta]

ok now I am doing the things again and here is the result of output of each
command till adding ions. At the time of executing the command grompp for
reading em.mdp file for ions.tpr generation, I am getting the following
error:-


Fatal error:
Syntax error - File PTR.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Everything's formed from particles" (Van der Graaf Generator)

here's a list of output , I obtained till the step of adding ion ??





O/P - pdb2gmx command:-
+++

Checking for duplicate atoms
Now there are 230 residues with 3606 atoms
Making bonds...
Number of bonds was 3646, now 3646
Generating angles, dihedrals and pairs...
Before cleaning: 9583 pairs
Before cleaning: 9678 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are  228 cmap torsion pairs
There are 9678 dihedrals,  618 impropers, 6593 angles
  9517 pairs, 3646 bonds and 0 virtual sites
Total mass 25776.218 a.m.u.
Total charge -2.000 e
Writing topology

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: GFP_enzmod1.pdb.
The Charmm27 force field and the spce water model are used.
- ETON ESAELP 

gcq#139: "I Wrapped a Newspaper Round My Head" (F. Zappa)



changes made in conf.gro file :-
+

  230THR   HG21 3601  -0.993   7.382   0.813
  230THR   HG22 3602  -0.976   7.242   0.730
  230THR   HG23 3603  -0.910   7.380   0.672
  230THR  C 3604  -1.255   7.279   0.449
  230THROT1 3605  -1.294   7.160   0.452
  230THROT2 3606  -1.337   7.205   0.529
1LIG C21  -0.905  -0.297  -0.859
1LIG C42  -0.546   1.023  -1.066
1LIG C53   0.009  -1.235  -0.411
1LIG C64   0.769   1.418  -0.818
1LIG C75   1.324  -0.840  -0.163
1LIG C86   1.704   0.487  -0.366
1LIG  P7   4.170  -0.099   0.400
1LIG  O8  -2.576   1.102   1.627
1LIG O19   2.986   0.872  -0.124
1LIG O2   10  -4.171   1.666   0.128
1LIG O3   11   4.434  -1.105  -0.839
1LIG O4   12   5.468   0.867   0.365
1LIG O5   13   3.920  -0.754   1.728
1LIG  N   14  -4.640  -1.030  -0.361
1LIG  C   15  -3.299  -0.614   0.075
1LIG C1   16  -2.331  -0.725  -1.128
1LIG C3   17  -3.413   0.823   0.594
1LIG  H   18  -2.714  -0.120  -1.963
1LIG H3   19  -2.321  -1.757  -1.509
1LIG H4   20  -5.279  -1.040   0.434
1LIG H5   21  -4.610  -1.988  -0.710
1LIG H6   22  -1.265   1.756  -1.419
1LIG H7   23  -0.275  -2.271  -0.254
1LIG H8   24   1.059   2.453  -0.978
1LIG H9   25   2.016  -1.600   0.183
1LIGH10   26  -2.667   2.031   1.929
1LIGH11   27   5.079  -1.836  -0.728
1LIGH12   28   6.314   0.538   0.737
1LIG H1   29  -4.984  -0.408  -1.078
1LIG H2   30  -2.958  -1.266   0.879
   5.23907   4.16174   3.66560



changes made in topol.top file:-
+++

;Include ligand topology
#include "PTR.itp"



[ molecules ]
; Compound#mols
Protein_chain_A 1
LIG 1

===

O/P - editconf command:-
++

ead 3636 atoms
Volume: 79.9234 nm^3, corresponds to roughly 35900 electrons
No velocities found
system size : 11.593 11.312  4.781 (nm)
diameter: 13.225   (nm)
center  :  0.967  7.015 -1.015 (nm)
box vectors :  5.239  4.162  3.666 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  :  79.92   (nm^3)
shift   :  6.645  0.598  8.627 (nm)
new center  :  7.612  7.612  7.612 (nm)
new box vectors : 15.225 15.225 15.225 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3529.00   (nm^3)

gcq#188: "Clickety Clickety Click" (System Manager From Hell)




O/P - genbox command:-


Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 9x9x9 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL (   3 atoms): 157464 residues
Calculating Overlap...
box_margin = 0.315
Removed 98544 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total ch

Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[Mark Abraham]

On 21/06/2011 2:51 PM, bharat gupta wrote:
ok now I am doing the things again and here is the result of output of 
each command till adding ions. At the time of executing the command 
grompp for reading em.mdp file for ions.tpr generation, I am getting 
the following error:-



Fatal error:
Syntax error - File PTR.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---

"Everything's formed from particles" (Van der Graaf Generator)

here's a list of output , I obtained till the step of adding ion ??


You haven't followed the steps of the tutorial well enough. 
Specifically, you've edited a .top or .itp file in the wrong place.


Mark
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[bharat gupta]

Now I changed the .top file in this way and I am getting this error now :-

change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

;Include ligand topology
#include "PTR.itp"

[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

=

error:-


Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 23220 of the 23220 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20092 of the 23220 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

---
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype LIG
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)





On Tue, Jun 21, 2011 at 1:56 PM, Mark Abraham wrote:

> On 21/06/2011 2:51 PM, bharat gupta wrote:
>
>> ok now I am doing the things again and here is the result of output of
>> each command till adding ions. At the time of executing the command grompp
>> for reading em.mdp file for ions.tpr generation, I am getting the following
>> error:-
>>
>>
>> Fatal error:
>> Syntax error - File PTR.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> --**-
>>
>> "Everything's formed from particles" (Van der Graaf Generator)
>>
>> here's a list of output , I obtained till the step of adding ion ??
>>
>
> You haven't followed the steps of the tutorial well enough. Specifically,
> you've edited a .top or .itp file in the wrong place.
>
> Mark
>
> --
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[Mark Abraham]

On 21/06/2011 3:03 PM, bharat gupta wrote:

Now I changed the .top file in this way and I am getting this error now :-

change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

;Include ligand topology
#include "PTR.itp"

[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

=

error:-


Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 23220 of the 23220 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20092 of the 23220 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

---
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype LIG
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---


You have to make an attempt to solve your own problems :-) We have 
better things to do than oversee every move you make. Follow that link 
and read about this issue.


Mark
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Re: [gmx-users] minimum image violation

[Kavyashree M]

Sir,

 I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I hope does
not cause serious trouble (as the minimum bond
length is of the order of 1 Angs) So can I make use
of this part of trajectory?

 I know that this part of the trajectory have been
arrived at through flawed interactions. But have any one
made such an attempt to analyze this?

Sorry again!

With regards
M. Kavyashree

On Tue, Jun 21, 2011 at 2:46 AM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear users,
>> I ran 100ns simulation for 4 proteins, 3 of them were
>> non covalent dimers in solution, but only 1 is a covalent
>> dimer connected by a disulphide bridge. I used monomers
>> to run the job.
>>Only in the case of covalent dimer I was getting severe
>> minimum image violation ie. out of 50001 data points,
>> 282 are <= 1.4nm
>> 280 are < 1.4nm
>> 144 are < 1.3nm
>> 79 are < 1.2nm
>> 28 are < 1.1nm
>> 4 < 1.0nm
>>
>> I agree that this is quite wrong but I wanted to know whether
>> any useful information can be gathered out of this simulation?
>>
>>
>
> Not likely.  Nearly 2% of the saved frames are unusable, indicating that
> potentially even more of the frames in the trajectory are useless, as well,
> and the dynamics that produced them are flawed.
>
>
>  In another data while calculating the energy terms it gives
>> nan (not a number error) for rmsd alone eg -
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>> --**--**
>> ---
>> Temperature 300  9e-05   -nan -0.000501989
>>  (K)
>>
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>> --**--**
>> ---
>> Pressure0.99914  0.027   -nan  0.0174391
>>  (bar)
>>
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>> --**--**
>> ---
>> Volume  517.755 0.0094   -nan   0.010871
>>  (nm^3)
>>  Initially i though some data points are missing but later
>> gmxcheck gives that all the data points are present.
>> now what could be the error?
>>
>> I had asked this question before and was instructed to check the
>> trajectory. I checked the rmsd rmsf of this with the other proteins
>> it similar but one of the segment has high rmsf compared to the other
>> proteins.
>>
>>
> My advice to you was to *watch* the trajectory to see where the PBC
> violations occurred, not run more analysis.  I doubt RMSF and RMSD will tell
> you anything useful.
>
> No one's been able to diagnose the problem based on this (continually
> posted) information.  If it's a useless trajectory, why bother?
>
> -Justin
>
>
>  Thanking you
>> With regards
>> M. Kavyashree
>>
>>
>>
>>
> --
> ==**==
>
> 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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>  posting!
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[gmx-users] implicit solvent system set up

[E. Nihal Korkmaz]

Dear all,

This may sound stupid, but just to make sure that I am right track about
implicit solvent simulations, the set up involves
pdb2gmx
editconf
grompp

I mean, we still need to define the box dimensions by editconf and apply
periodicity, right?
Besides, what type of ensemble would be a good choice (NPT, NVT, etc)?

Best,

-- 
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   kork...@wisc.edu
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[bharat gupta]

I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr

I am getting a charge of  -9.71e-01


Since the charge has to be in whole number, what shall I do in this case.
(The ligand that I am using is phosphotyrosine)


On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham wrote:

> On 21/06/2011 3:03 PM, bharat gupta wrote:
>
>> Now I changed the .top file in this way and I am getting this error now :-
>>
>> change :- ; Include forcefield parameters
>> #include "charmm27.ff/forcefield.itp"
>>
>> ;Include ligand topology
>> #include "PTR.itp"
>>
>> [ moleculetype ]
>> ; Namenrexcl
>> Protein_chain_A 3
>>
>> =
>>
>> error:-
>>
>>
>> Ignoring obsolete mdp entry 'title'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
>> Generated 23220 of the 23220 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 20092 of the 23220 1-4 parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>>
>> --**-
>> Program grompp, VERSION 4.5.4
>> Source code file: toppush.c, line: 1987
>>
>> Fatal error:
>> No such moleculetype LIG
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> --**-
>>
>
> You have to make an attempt to solve your own problems :-) We have better
> things to do than oversee every move you make. Follow that link and read
> about this issue.
>
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>  posting!
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>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] minimum image violation

[Mark Abraham]

On 21/06/2011 3:43 PM, Kavyashree M wrote:

Sir,

 I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I hope does
not cause serious trouble (as the minimum bond
length is of the order of 1 Angs) So can I make use
of this part of trajectory?


The purpose of the minimum image convention is to help model the real 
conditions under which your protein exists. The usual case is one of 
(effectively) infinite dilution. However, if you have a protein atom 
that is influenced by an atom of a periodic image of the protein, then 
you are not close to modeling infinite dilution. Arguably, a water atom 
that can see two different periodic images is also unrealistic, but 
probably this will be a lower-order effect, and vary from case to case.


So as soon as you get a violation, further data about your system is 
tainted from the previous existence of unrealistic conditions. Even just 
looking at the first part of the simulation before the violation 
(assuming it has equilibrated properly so far) is questionable, because 
you have imposed on its ensemble the restriction that it cannot grow 
larger than a given diameter for a given orientation. It's up to you to 
judge whether the effect is small enough to ignore, and that depends on 
lots of things we can't know.


There exist a large number of areas of biomolecular simulations where 
our inability to exhaustively sample ensembles has limited our ability 
to quantify the size of various effects. The effect of violations of 
minimum-image conventions on proteins is one of those areas.


The important lesson here is that doing a simulation blindly runs a 
large risk of wasting resources. Ongoing attention to lots of details is 
important. As in many fields of human endeavour, there are lots of 
lessons that have been written in the blood of unfortunate people before 
you. In research, there will be lessons written in your blood. The trick 
is to learn from the former in order to minimize the latter :-)


Mark
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[bharat gupta]

So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-

Step=1, Dmax= 1.0e-02 nm, Epot=  1.36889e+09 Fmax= 1.97591e+11, atom=
1248
Step=2, Dmax= 1.2e-02 nm, Epot=  5.46814e+07 Fmax= 3.57239e+09, atom=
972
Step=3, Dmax= 1.4e-02 nm, Epot=  8.68244e+06 Fmax= 5.80655e+08, atom=
1253
Step=4, Dmax= 1.7e-02 nm, Epot=  3.33619e+06 Fmax= 9.98000e+07, atom=
1248
Step=5, Dmax= 2.1e-02 nm, Epot=  2.30163e+06 Fmax= 1.19057e+07, atom=
1253
Step=6, Dmax= 2.5e-02 nm, Epot=  2.07254e+06 Fmax= 3.20568e+06, atom=
1304
Step=7, Dmax= 3.0e-02 nm, Epot=  1.97667e+06 Fmax= 1.59513e+06, atom=
1045
Step=8, Dmax= 3.6e-02 nm, Epot=  1.85877e+06 Fmax= 8.25518e+05, atom=
3616
Step=9, Dmax= 4.3e-02 nm, Epot=  1.66148e+06 Fmax= 7.69483e+05, atom=
3616
Step=   10, Dmax= 5.2e-02 nm, Epot=  1.43976e+06 Fmax= 6.47087e+05, atom=
3616
Step=   11, Dmax= 6.2e-02 nm, Epot=  1.16869e+06 Fmax= 6.39015e+05, atom=
3616
Step=   12, Dmax= 7.4e-02 nm, Epot=  8.84664e+05 Fmax= 5.75494e+05, atom=
3616
Step=   13, Dmax= 8.9e-02 nm, Epot=  6.62825e+05 Fmax= 1.01984e+07, atom=
47956

step 14: Water molecule starting at atom 47956 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   15, Dmax= 5.3e-02 nm, Epot=  5.67330e+05 Fmax= 5.36987e+05, atom=
36166
Step=   16, Dmax= 6.4e-02 nm, Epot=  3.51341e+05 Fmax= 4.19647e+05, atom=
3619
Step=   17, Dmax= 7.7e-02 nm, Epot=  6.34731e+04 Fmax= 1.56555e+06, atom=
3616
Step=   18, Dmax= 9.2e-02 nm, Epot= -2.03364e+04 Fmax= 4.60916e+05, atom=
3616
Step=   19, Dmax= 1.1e-01 nm, Epot= -3.50504e+05 Fmax= 1.53090e+06, atom=
213514

step 20: Water molecule starting at atom 213514 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   20, Dmax= 1.3e-01 nm, Epot= -4.11692e+05 Fmax= 4.49357e+05, atom=
3619
Step=   21, Dmax= 1.6e-01 nm, Epot= -4.87207e+05 Fmax= 3.39700e+07, atom=
3629
Step=   22, Dmax= 1.9e-01 nm, Epot= -7.85503e+05 Fmax= 3.56083e+05, atom=
3619

step 23: Water molecule starting at atom 206593 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 23: Water molecule starting at atom 212776 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=   23, Dmax= 2.3e-01 nm, Epot=  1.95863e+09 Fmax= 6.76309e+11, atom=
3633
step 24: Water molecule starting at atom 212776 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   25, Dmax= 5.8e-02 nm, Epot= -9.28980e+05 Fmax= 2.81692e+05, atom=
362976

step 26: Water molecule starting at atom 42463 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   27, Dmax= 3.5e-02 nm, Epot= -1.03111e+06 Fmax= 2.76677e+05, atom=
36293
Step=   28, Dmax= 4.1e-02 nm, Epot= -1.14733e+06 Fmax= 2.66398e+05, atom=
3629
Step=   29, Dmax= 5.0e-02 nm, Epot= -1.26821e+06 Fmax= 2.51779e+05, atom=
3629
Step=   30, Dmax= 6.0e-02 nm, Epot= -1.42873e+06 Fmax= 2.31393e+05, atom=
3629
Step=   31, Dmax= 7.2e-02 nm, Epot= -1.59623e+06 Fmax= 3.53379e+06, atom=
3633

step 32: Water molecule starting at atom 292885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   33, Dmax= 4.3e-02 nm, Epot= -1.62300e+06 Fmax= 2.45780e+05, atom=
361985
Step=   34, Dmax= 5.2e-02 nm, Epot= -1.75124e+06 Fmax= 2.87155e+05, atom=
213958
Step=   35, Dmax= 6.2e-02 nm, Epot= -1.86014e+06 Fmax= 6.76483e+05, atom=
3634

step 36: Water molecule starting at atom 256024 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   36, Dmax= 7.4e-02 nm, Epot= -1.91639e+06 Fmax= 2.49523e+05, atom=
3619
Step=   37, Dmax= 8.9e-02 nm, Epot= -2.11154e+06 Fmax= 4.87466e+05, atom=
3636
Step=   38, Dmax= 1.1e-01 nm, Epot= -2.20858e+06 Fmax= 1.92308e+05, atom=
3629
Step=   40, Dmax= 6.4e-02 nm, Epot= -2.34036e+06 Fmax= 3.07614e+06, atom=
3634
Step=   41, Dmax= 7.7e-02 nm, Epot= -2.36181e+06 Fmax= 1.95100e+05, atom=
3634
Step=   42, Dmax= 9.2e-02 nm, Epot= -2.55367e+06 Fmax= 1.66837e+05, atom=
3629
Step=   43, Dmax= 1.1e-01 nm, Epot= -2.67052e+06 Fmax= 1.01067e+07, atom=
3618
Step=   44, Dmax= 1.3e-01 nm, Epot= -2.76975e+06 Fmax= 2.25183e+05, atom=
3618
Step=   45, Dmax= 1.6e-01 nm, Epot= -2.95070e+06 Fmax= 5.66364e+05, atom=
3614

step 46: Water molecule starting at atom 249877 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 46: Water molecule starting at atom 85966 can not be set

[gmx-users] cosine content

[Kavyashree M]

Dear users,

   When are checking the cosine content of a PC, (Pls. Correct me if I am
wrong)
This is the command we use -
"g_analyze -f .xvg -cc .xvg"

and for first PC output says -
Cosine content of set 1 with 0.5 periods: ---

for nth PC also it says -
Cosine content of set 1 with 0.5 periods: ---

Where does this get the information that the cosine wave that it has to
fit is half the eigenvector rank? is it "y axis label" ?

Thank you
With regards
M. Kavyashree
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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[Mark Abraham]

On 21/06/2011 4:15 PM, bharat gupta wrote:
I fixed it ... but now after using the command : grompp -f em.mdp -c 
solv.gro -p topol.top -o ions.tpr


I am getting a charge of  -9.71e-01


Since the charge has to be in whole number, what shall I do in this 
case. (The ligand that I am using is phosphotyrosine)


OK, that's what I expected you were doing - truncating the output and 
not rounding appropriately. See 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic again - 
I've updated it to deal with this issue more explicitly.


Mark



On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham > wrote:


On 21/06/2011 3:03 PM, bharat gupta wrote:

Now I changed the .top file in this way and I am getting this
error now :-

change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

;Include ligand topology
#include "PTR.itp"

[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

=

error:-


Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 23220 of the 23220 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20092 of the 23220 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

---
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype LIG
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


You have to make an attempt to solve your own problems :-) We have
better things to do than oversee every move you make. Follow that
link and read about this issue.


Mark
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



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Re: [gmx-users] Re: Error during executing the protein ligand tutorial

[Mark Abraham]

On 21/06/2011 4:33 PM, bharat gupta wrote:
So, after adding 1 NA ion, I started with energy mimization, but I am 
getting the following error after md run command :-


Please search for help first.

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Mark

Step=1, Dmax= 1.0e-02 nm, Epot=  1.36889e+09 Fmax= 1.97591e+11, 
atom= 1248
Step=2, Dmax= 1.2e-02 nm, Epot=  5.46814e+07 Fmax= 3.57239e+09, 
atom= 972
Step=3, Dmax= 1.4e-02 nm, Epot=  8.68244e+06 Fmax= 5.80655e+08, 
atom= 1253
Step=4, Dmax= 1.7e-02 nm, Epot=  3.33619e+06 Fmax= 9.98000e+07, 
atom= 1248
Step=5, Dmax= 2.1e-02 nm, Epot=  2.30163e+06 Fmax= 1.19057e+07, 
atom= 1253
Step=6, Dmax= 2.5e-02 nm, Epot=  2.07254e+06 Fmax= 3.20568e+06, 
atom= 1304
Step=7, Dmax= 3.0e-02 nm, Epot=  1.97667e+06 Fmax= 1.59513e+06, 
atom= 1045
Step=8, Dmax= 3.6e-02 nm, Epot=  1.85877e+06 Fmax= 8.25518e+05, 
atom= 3616
Step=9, Dmax= 4.3e-02 nm, Epot=  1.66148e+06 Fmax= 7.69483e+05, 
atom= 3616
Step=   10, Dmax= 5.2e-02 nm, Epot=  1.43976e+06 Fmax= 6.47087e+05, 
atom= 3616
Step=   11, Dmax= 6.2e-02 nm, Epot=  1.16869e+06 Fmax= 6.39015e+05, 
atom= 3616
Step=   12, Dmax= 7.4e-02 nm, Epot=  8.84664e+05 Fmax= 5.75494e+05, 
atom= 3616
Step=   13, Dmax= 8.9e-02 nm, Epot=  6.62825e+05 Fmax= 1.01984e+07, 
atom= 47956


step 14: Water molecule starting at atom 47956 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   15, Dmax= 5.3e-02 nm, Epot=  5.67330e+05 Fmax= 5.36987e+05, 
atom= 36166
Step=   16, Dmax= 6.4e-02 nm, Epot=  3.51341e+05 Fmax= 4.19647e+05, 
atom= 3619
Step=   17, Dmax= 7.7e-02 nm, Epot=  6.34731e+04 Fmax= 1.56555e+06, 
atom= 3616
Step=   18, Dmax= 9.2e-02 nm, Epot= -2.03364e+04 Fmax= 4.60916e+05, 
atom= 3616
Step=   19, Dmax= 1.1e-01 nm, Epot= -3.50504e+05 Fmax= 1.53090e+06, 
atom= 213514


step 20: Water molecule starting at atom 213514 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   20, Dmax= 1.3e-01 nm, Epot= -4.11692e+05 Fmax= 4.49357e+05, 
atom= 3619
Step=   21, Dmax= 1.6e-01 nm, Epot= -4.87207e+05 Fmax= 3.39700e+07, 
atom= 3629
Step=   22, Dmax= 1.9e-01 nm, Epot= -7.85503e+05 Fmax= 3.56083e+05, 
atom= 3619


step 23: Water molecule starting at atom 206593 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 23: Water molecule starting at atom 212776 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=   23, Dmax= 2.3e-01 nm, Epot=  1.95863e+09 Fmax= 6.76309e+11, 
atom= 3633

step 24: Water molecule starting at atom 212776 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   25, Dmax= 5.8e-02 nm, Epot= -9.28980e+05 Fmax= 2.81692e+05, 
atom= 362976


step 26: Water molecule starting at atom 42463 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   27, Dmax= 3.5e-02 nm, Epot= -1.03111e+06 Fmax= 2.76677e+05, 
atom= 36293
Step=   28, Dmax= 4.1e-02 nm, Epot= -1.14733e+06 Fmax= 2.66398e+05, 
atom= 3629
Step=   29, Dmax= 5.0e-02 nm, Epot= -1.26821e+06 Fmax= 2.51779e+05, 
atom= 3629
Step=   30, Dmax= 6.0e-02 nm, Epot= -1.42873e+06 Fmax= 2.31393e+05, 
atom= 3629
Step=   31, Dmax= 7.2e-02 nm, Epot= -1.59623e+06 Fmax= 3.53379e+06, 
atom= 3633


step 32: Water molecule starting at atom 292885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   33, Dmax= 4.3e-02 nm, Epot= -1.62300e+06 Fmax= 2.45780e+05, 
atom= 361985
Step=   34, Dmax= 5.2e-02 nm, Epot= -1.75124e+06 Fmax= 2.87155e+05, 
atom= 213958
Step=   35, Dmax= 6.2e-02 nm, Epot= -1.86014e+06 Fmax= 6.76483e+05, 
atom= 3634


step 36: Water molecule starting at atom 256024 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   36, Dmax= 7.4e-02 nm, Epot= -1.91639e+06 Fmax= 2.49523e+05, 
atom= 3619
Step=   37, Dmax= 8.9e-02 nm, Epot= -2.11154e+06 Fmax= 4.87466e+05, 
atom= 3636
Step=   38, Dmax= 1.1e-01 nm, Epot= -2.20858e+06 Fmax= 1.92308e+05, 
atom= 3629
Step=   40, Dmax= 6.4e-02 nm, Epot= -2.34036e+06 Fmax= 3.07614e+06, 
atom= 3634
Step=   41, Dmax= 7.7e-02 nm, Epot= -2.36181e+06 Fmax= 1.95100e+05, 
atom= 3634
Step=   42, Dmax= 9.2e-02 nm, Epot= -2.55367e+06 Fmax= 1.66837e+05, 
atom= 3629
Step=   43, Dmax= 1.1e-01 nm, Epot= -2.67052e+06 Fmax= 1.01067e+07, 
atom= 3618
Step=   44, Dmax= 1.3e-01 nm, Epot= -2.76975e+06 Fmax= 2.25183e+05, 
atom= 3618
Step=   45, Dmax= 1.6e-01 nm, Epot= -2.95070e+06 Fmax= 5.66364e+05, 
a