RE: [gmx-users] g_analyze - negative parameters

[Berk Hess]

Hi,

Your data might have intrinsically strange time correlations,
but the chances are high that you have not sampled enough.
I would first also try the g_analyze of Gromacs 4.0, I have improved
some subtleties in the fitting weights there, which can help in certain
unstable cases.
But tau1 seems extremely long, or does your input have even longer times?

Berk

> From: maximilian.andr...@tu-dortmund.de
> To: gmx-users@gromacs.org
> Date: Mon, 1 Feb 2010 19:49:17 +0100
> Subject: [gmx-users] g_analyze - negative parameters
> 
> Dear Gromacs-Users,
> 
> I've been trying to figure out g_analyze for a while now (having read
> the manual references and papers), but I still haven't found out what
> a negative parameter obtained during fitting means. It's clear that
> when Tau2 is longer than the total simulation time the sampling is
> bad, but I don't know how to interpret a negative parameter and how it
> affects the sampling, as can be seen from the output excerpt obtained
> from the following command (in Gromacs 3.x):
> 
> g_analyze -f data.xvg --ee data_ee.xvg
>  
> a fitted parameter is negative
> invalid fit:  e.e. 0.9166  a 0.0376076  tau1 -21618.1  tau2 383059
> Set   1:  err.est. 61.1951  a 1  tau1 1.63958e+09  tau2 0
> 
> I'm interested in the average value and the error estimate, but I
> obviously would like to know if my data is good. I guess that since
> Tau2 is set to zero, I only have the short time correlation, and not the
> long time one.
> 
> Thanks in advance for your time!
> 
> Best regards,
> 
> Maximilian
> -- 
> Dortmund University of Technology
> Department of Chemistry
> Physical Chemistry I  -  Biophysical Chemistry
> Otto-Hahn-Str. 6
> D-44227 Dortmund
> Germany
> 
> Office:   C1-06 room 176
> Phone:  +49 231 755 3916
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[gmx-users] Hydrogen bond tutorial

[leila karami]

Dear all

I want to do Hydrogen bond analysis for my MD data (protein-dna
interaction).
If anybody know the tutorial regarding that, please let me know.

Any help will highly appreciated!
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Re: [gmx-users] Regarding Trjconv.and ligand -protein complex simulation.......

[Mark Abraham]

On 02/02/10 16:50, PAVAN PAYGHAN wrote:

Thnx for replying
A]
As i hv mentioned previously that in  my simulation  g_rms suggests it
has some large peaks ,so applied trjconv with
-pbc nojump now ...
  there are no peaks in rmsd its oky but in vmd it showed that water is
not having defined box so how to tackle this situation..
1.which -pbc option u suggests for this situation


Read trjconv -h, create a test case with only a few frames, and try out 
things that seem reasonable.



2.is  it possible to use two -pbc options together?


No, but it is normal to consider using several iterates trjconv if you 
want to massage things to look right to you.



3.is  it possible to modify the .xtc that i have generated
with -nojump further to have defined box.


Probably, whatever you mean by that.


B]
my next question is with gromacs version 3.3.2
  if im using NMR structure i need to give -ignh  option in pdb2gmx to
ignore hydrogens or it will be taken care of  automatically.


Did you read pdb2gmx -h, and then try it and see? Experience is the best 
teacher.



  C]
  Will u please give me any tutorial on ligand-dna/protein simulation
either with PRODRG or ANTCHAMBER for drug input preparation.


Please start by searching the GROMACS webpage and Google first. You may 
discover alternatives to your preconceived solutions.


Mark
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Re: [gmx-users] H2 topology

[Mark Abraham]

On 02/02/10 14:23, 011013021-Jyotsna wrote:


Dear David,
Thank you very much for your help.
As per the literature am following , it is mentioned that the bond
distance used is 0.7 Angstrom. Where do I incorporate the bond distance
parameter in the topology file?


See example in chapter 5 of the manual.


The problem am facing is that , I am not
very clear as to if the distance is between the two Hydrogen atoms of
btween the dummy atom and each of the Hydrogen atoms in either side, in
which case the total distance becomes 1.4 A.


Surely the text of the original article is more clear than that. In any 
case, from where did you get the number 0.7439756 in your topology?



When i mention the bond distance in the topology file , should it be
placed under Bond or constraint?


The article surely specifies the nature of the bonded interaction. Work 
out what that is, and then consider the tables in section 5.7.1.


Science in general and computational science in particular is very 
exacting. For your own sake, please cultivate that habit :-)


Mark


Thank you,
Jyotsna


Re: [gmx-users] H2 topology
David van der Spoel
Mon, 01 Feb 2010 04:02:06 -0800

On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:
Dear all,

I want to run a simulation for an enzyme. It demands me to incorporate a
Molecular hydrogen Topology with a dummy atom in between in the
simulation in order to study the path of hydrogen in it.The problem is ,
the topology file I built induces many errors when i come to the energy
minimization step. The version of gromacs I am using is 4.0. The
topology file I built is as follows



[ moleculetype ]
;name nrexcl
H2 3

[ atoms ]
; nr type resnr residu atom cgnr charge mass ; total charge
1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
3 DUM 1 H2 DUM 1 -0.950 0.000

[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.7439756


When ever I insert the hydrogen+dummy atom topology in the protein's
.gro file, an error is generated regarding mismatch of residues or the
dummy atom having mass 0 .

I would be really grateful if anyone could provide me the hydrogen
molecule topology and give some pointers towards it.


Please print the error message in your mail.

Topology look OK, but you need to add a bond or constraint.
Also the constant probably has to be 0.5 since you want the vsite in the
center of the two atoms.


Thank you,

Jyotsna



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[gmx-users] Regarding Trjconv.and ligand -protein complex simulation.......

[PAVAN PAYGHAN]

Thnx for replying
A]
As i hv mentioned previously that in  my simulation  g_rms suggests it has
some large peaks ,so applied trjconv with
-pbc nojump now ...
 there are no peaks in rmsd its oky but in vmd it showed that water is not
having defined box so how to tackle this situation..
1.which -pbc option u suggests for this situation
2.is it possible to use two -pbc options together?
3.is it possible to modify the .xtc that i have generated with -nojump
further to have defined box.

B]
my next question is with gromacs version 3.3.2
 if im using NMR structure i need to give -ignh  option in pdb2gmx to ignore
hydrogens or it will be taken care of  automatically.

 C]
 Will u please give me any tutorial on ligand-dna/protein simulation either
with PRODRG or ANTCHAMBER for drug input preparation.
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[gmx-users] H2 topology

[011013021-Jyotsna]

Dear David,
Thank you very much for your help.
As per the literature am following , it is mentioned that 
the bond distance used is 0.7 Angstrom. Where do I 
incorporate the bond distance parameter in the topology 
file? The problem am facing is that , I am not very clear 
as to if the distance is between the two Hydrogen atoms of 
btween the dummy atom and each of the Hydrogen atoms in 
either side, in which case the total distance becomes 1.4 
A.
When i mention the bond distance in the topology file  , 
should it be placed under Bond or constraint?



Thank you,
Jyotsna


Re: [gmx-users] H2 topology
David van der Spoel
Mon, 01 Feb 2010 04:02:06 -0800

On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:
Dear all,

I want to run a simulation for an enzyme. It demands me to 
incorporate a
Molecular hydrogen Topology with a dummy atom in between 
in the
simulation in order to study the path of hydrogen in 
it.The problem is ,
the topology file I built induces many errors when i come 
to the energy
minimization step. The version of gromacs I am using is 
4.0. The

topology file I built is as follows



[ moleculetype ]
;name nrexcl
H2 3

[ atoms ]
; nr type resnr residu atom cgnr charge mass ; total 
charge

1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
3 DUM 1 H2 DUM 1 -0.950 0.000

[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.7439756


When ever I insert the hydrogen+dummy atom topology in the 
protein's
.gro file, an error is generated regarding mismatch of 
residues or the

dummy atom having mass 0 .

I would be really grateful if anyone could provide me the 
hydrogen

molecule topology and give some pointers towards it.


Please print the error message in your mail.

Topology look OK, but you need to add a bond or 
constraint.
Also the constant probably has to be 0.5 since you want 
the vsite in the center of the two atoms.



Thank you,

Jyotsna


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Re: [gmx-users] PCA tutorial

[Justin A. Lemkul]

rituraj purohit wrote:

Dear friends,
I want to do PCA for my MD data.
If anybody know the tutorial regarding PCA, please let me know.
Thanks in advanced



There's not so much a tutorial for PCA as there is a sequence of a few commands. 
 Tsjerk's lysozyme tutorial has an excellent section on PCA:


http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/analysis1.html

-Justin


Regard
Rohan


--


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] PCA tutorial

[rituraj purohit]

topology in the protein's
> > .gro file, an error is generated regarding mismatch of residues or the
> > dummy atom having mass 0 .
> >
> > I would be really grateful if anyone could provide me the hydrogen
> > molecule topology and give some pointers towards it.
> >
>
> Please print the error message in your mail.
>
> Topology look OK, but you need to add a bond or constraint.
> Also the constant probably has to be 0.5 since you want the vsite in the
> center of the two atoms.
>
>
> > Thank you,
> >
> > Jyotsna
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
>
>
> --
>
> Message: 5
> Date: Mon, 1 Feb 2010 12:16:02 +
> From: Catarina Nunes 
> Subject: [gmx-users] tutorial for ionic liquid
> To: gmx-users@gromacs.org
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
> Do you have any tutorial for ?
> Best regards
> Catarina
>
>
> --
>
> Message: 6
> Date: Mon, 01 Feb 2010 07:18:51 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] tutorial for ionic liquid
> To: Discussion list for GROMACS users 
> Message-ID: <4b66c6ab.2070...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Catarina Nunes wrote:
> > Dear all,
> > Do you have any tutorial for ?
> > Best regards
> > Catarina
>
> Gromacs tutorials can be found at:
>
> http://www.gromacs.org/Documentation/Tutorials
>
> If you don't find it there, try Google.  If you don't find it there, it
> probably
> doesn't exist :)
>
> -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
>
> 
>
>
> --
>
> Message: 7
> Date: Mon, 1 Feb 2010 05:05:31 -0800 (PST)
> From: oguz gurbulak 
> Subject: [gmx-users] non-equilibrium MD simulations
> To: gmx-users@gromacs.org
> Message-ID: <547100.67241...@web36302.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
>
> I'm searching for a  non-equilibrium MD tutorial done with Gromacs. Could
> you please help me to find a NEMD tutorial ?
>
> Thank in advance .
>
>
>
>
>
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100201/ff079c22/attachment-0001.html
>
> --
>
> Message: 8
> Date: Mon, 01 Feb 2010 08:08:02 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] non-equilibrium MD simulations
> To: Discussion list for GROMACS users 
> Message-ID: <4b66d232.3020...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> oguz gurbulak wrote:
> > Dear All,
> >
> > I'm searching for a  non-equilibrium MD tutorial done with Gromacs.
> > Could you please help me to find a NEMD tutorial ?
> >
>
> "Non-equilibrium" can encompass a variety of topics, so if you want
> specific
> advice, you'll have to be more specific.  And, as I just mentioned to
> someone else:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-February/048498.html
>
> -Justin
>
> > Thank in advance .
> >
> >
> >
> >
>
> --
> 
>
> 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
>
> 
>
>
> --
>
>
> --
> gmx-users mailing list
> gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 70, Issue 5
> 
>
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[gmx-users] g_analyze - negative parameters

[Maximilian Andrews]

Dear Gromacs-Users,

I've been trying to figure out g_analyze for a while now (having read
the manual references and papers), but I still haven't found out what
a negative parameter obtained during fitting means. It's clear that
when Tau2 is longer than the total simulation time the sampling is
bad, but I don't know how to interpret a negative parameter and how it
affects the sampling, as can be seen from the output excerpt obtained
from the following command (in Gromacs 3.x):

g_analyze -f data.xvg --ee data_ee.xvg
 
a fitted parameter is negative
invalid fit:  e.e. 0.9166  a 0.0376076  tau1 -21618.1  tau2 383059
Set   1:  err.est. 61.1951  a 1  tau1 1.63958e+09  tau2 0

I'm interested in the average value and the error estimate, but I
obviously would like to know if my data is good. I guess that since
Tau2 is set to zero, I only have the short time correlation, and not the
long time one.

Thanks in advance for your time!

Best regards,

Maximilian
-- 
Dortmund University of Technology
Department of Chemistry
Physical Chemistry I  -  Biophysical Chemistry
Otto-Hahn-Str. 6
D-44227 Dortmund
Germany

Office:   C1-06 room 176
Phone:  +49 231 755 3916
Fax:+49 231 755 3901

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Re: [gmx-users] [OT] Software package for discontinuous molecular dynamics? (DMD)

[David van der Spoel]

On 2/1/10 4:32 PM, ms wrote:

Hi,

Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.

To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more-or-less standard software package for that?

thank you!
m.

Can you be more specific please?

--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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[gmx-users] [OT] Software package for discontinuous molecular dynamics? (DMD)

[ms]

Hi,

Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.

To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more-or-less standard software package for that?

thank you!
m.
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RE: [gmx-users] Re: density problems when switching from md to sd integrator

[Berk Hess]

Hi,

This force field was designed to be used with constraints.
First try running with constraints set to all-bonds and without -DFLEXIBLE and 
check
the densities again.

Berk

> Date: Mon, 1 Feb 2010 16:58:44 +0100
> From: ana...@fundp.ac.be
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: density problems when switching from md to sd
> integrator
> 
> I have changed tau_t=0.2 for 1.0 but the density is not restored. I have 
> tried with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548)
> , tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion 
> coefficient is indeed half of that with md with sd and tau_t=0.2 (0.71 vs. 
> 1.48 10-5 cm2/s)
> and about the same with tau_t=1.0 (1.57 10-5 cm2/s). Water is less affected 
> (1009 g/L with md and 1007 g/L with sd and tau_t=0.2). What is the reason why 
> the density is lowered?
> 
> Here is the .mdp file (for the simulation with md, tau_t=0.1):
> 
> title =  cyclohexane
> cpp =  /lib/cpp -traditional 
> define  =  -DFLEXIBLE
> constraints =  none
> integrator  =  sd
> dt  =  0.001  ; fs !
> nsteps  =  200; total 2000 ps.
> nstcomm =  1
> nstxout =  1000
> nstvout =  1000
> nstfout =  0
> nstlog  =  500
> nstenergy   =  500
> nstlist =  10 
> ns_type =  grid
> rlist   =  1.0
> coulombtype   =  PME
> rcoulomb=  1.0
> rvdw=  1.4
> fourierspacing=  0.12
> fourier_nx=  0
> fourier_ny=  0
> fourier_nz=  0
> pme_order =  6
> ewald_rtol=  1e-5
> optimize_fft  =  yes
> energygrps=  system
> ; Berendsen temperature coupling is on in three groups
> Tcoupl  =  berendsen
> tau_t   = 0.2
> tc_grps   = System 
> ref_t   = 298
> ; Pressure coupling is on
> Pcoupl  =  berendsen
> pcoupltype  =  isotropic
> tau_p   =  0.5
> compressibility =  11.2e-5
> ref_p   =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel =  no
> gen_temp=  298.0
> gen_seed=  173529
> ; Energy group exclusion
> energygrp_excl  =  
> freezegrps  =  
> freezedim   =  
> ; Non-equilibrium Thermodynamics
> acc_grps  =  
> accelarate=  
> ; center of mass
> comm_mode   = 
> comm_grps   =
> 
> > Dear Aymeric:
> >
> > 1. Can we please see the entire .mdp files for both simulations? I  
> > suggest that you use a tau_t=1.0 (0.2 is probably over-damped).
> >
> > 2. Although any value of tau_t should still produce the correct  
> > equilibria, your diffusion rates and your overall sampling may be  
> > slower with sd tau_t=0.2 than they are with md.
> >
> > 3. Can you reproduce this effect with a box of water?
> >
> >> -- original message --
> >>
> >> I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
> >> compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
> >> After equilibration and NPT simulation, the system reaches the proper
> >> density reported for the model (791g/L). When I switch to a stochastic
> >> integrator (with inverse friction coeff. tau_t=0.2 ps) the density
> >> rapidly falls to about 765g/L, the potential energy increases, while
> >> temperature and pressure fluctuate much more around their specified
> >> values. I intend to use this box of cyclohexane for solvation free
> >> energy calculations. Can anyone explain what is going on?
> >> Thanks in advance
> >>
> >> Aymeric
> 
  
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[gmx-users] Re: density problems when switching from md to sd integrator

[Aymeric Naômé]

I have changed tau_t=0.2 for 1.0 but the density is not restored. I have tried 
with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548)
, tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion 
coefficient is indeed half of that with md with sd and tau_t=0.2 (0.71 vs. 1.48 
10-5 cm2/s)
and about the same with tau_t=1.0 (1.57 10-5 cm2/s). Water is less affected 
(1009 g/L with md and 1007 g/L with sd and tau_t=0.2). What is the reason why 
the density is lowered?

Here is the .mdp file (for the simulation with md, tau_t=0.1):

title   =  cyclohexane
cpp =  /lib/cpp -traditional 
define  =  -DFLEXIBLE

constraints =  none
integrator  =  sd
dt  =  0.001; fs !
nsteps  =  200  ; total 2000 ps.
nstcomm =  1
nstxout =  1000
nstvout =  1000
nstfout =  0
nstlog  =  500
nstenergy   =  500
nstlist =  10 
ns_type =  grid

rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes
energygrps  =  system
; Berendsen temperature coupling is on in three groups
Tcoupl  =  berendsen
tau_t   = 0.2
tc_grps		= System 
ref_t   = 298
; Pressure coupling is on

Pcoupl  =  berendsen
pcoupltype  =  isotropic
tau_p   =  0.5
compressibility =  11.2e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  no
gen_temp=  298.0
gen_seed=  173529
; Energy group exclusion
energygrp_excl  =  
freezegrps  =  
freezedim   =  
; Non-equilibrium Thermodynamics
acc_grps	=  
accelarate	=  
; center of mass
comm_mode   = 
comm_grps   =



Dear Aymeric:

1. Can we please see the entire .mdp files for both simulations? I  
suggest that you use a tau_t=1.0 (0.2 is probably over-damped).


2. Although any value of tau_t should still produce the correct  
equilibria, your diffusion rates and your overall sampling may be  
slower with sd tau_t=0.2 than they are with md.


3. Can you reproduce this effect with a box of water?


-- original message --

I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
After equilibration and NPT simulation, the system reaches the proper
density reported for the model (791g/L). When I switch to a stochastic
integrator (with inverse friction coeff. tau_t=0.2 ps) the density
rapidly falls to about 765g/L, the potential energy increases, while
temperature and pressure fluctuate much more around their specified
values. I intend to use this box of cyclohexane for solvation free
energy calculations. Can anyone explain what is going on?
Thanks in advance

Aymeric


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Re: [gmx-users] perl scripts to convert CHARMM ff in GROMACS

[Mark Abraham]

On 02/02/10 01:29, ABEL Stephane 175950 wrote:

Hi GMXusers

I am testing the parameters of CHARMM, it works fine for lipids and protein. This 
is a great job, thanks to the devellopers But i would like to add some new 
molecule for solvent (e.g. for TFE) The atom types of TFE are present in the 
ffcharmm27bon.itp available in latest port (c32b1_release_1.1.zip, dowloaded 
http://www.dbb.su.se/User:Bjelkmar/Ffcharmm), unfortunately several bonded 
parameters (for example  F3-CF3, CF3-CT2x, etc..) are missing in ffcharmm27bon.itp 
file. So I need to convert the missing parameters into gromacs format. In website 
(URL:http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), I have 
found that several perl scripts exist for the conversion charmm-->  gromacs. 
The archive is corrupted so, I cannot unpacked the directory to obtain the files.

Where I can find these scripts


Emailed off-list. This package is now deprecated.

Mark
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[gmx-users] Fwd: Help for REMD

[Mark Abraham]

Please keep GROMACS correspondence on the mailing list. Nobody here is a 
private tutor unless you're paying them.


 Original Message 
Subject: Help for REMD
Date: Mon, 01 Feb 2010 14:58:08 +0200 (EET)
From: Murat Erman OGUZ 
To: mark.abra...@anu.edu.au

Dear Mr.Mark Abraham
I am Erman Oguz from Turkey Hacettepe University.
I have a problem about Replica Excahange Method on Gromacs.
ı hope you can help me.

I am trying to perform replica exchange MD on a 'protein in
water' system. I have to perform the REMD simulation with 64 different
temperatures.As per advise on wiki,I equilibrated the system at
respective temperatures (total of 64 equilibration simulations in 200 ps).
After this I generated "tpr files" from the equilibrated structure.
when I submit final job for REMD with following command-line

command line: mpirun -np 64 mdrun -multi 64 -replex 1000 -s *_.tpr .

it gives error that :

t=29.802 ps Water molecule starting at atom 5902 can not be settled.
check for bad contacs and/or reduce time step.

what can I do and how can I do... please help me...


You should start by searching on the GROMACS webpage errors page. The 
reasons for this kind of error are clearly described there, and are 
likely to have nothing to with REMD as such. If they were, you'll have 
to provide much more data for anyone to help.


You should try your .tpr files in a non-replica simulation and see which 
are broken and thus what to do about it. Probably you've not 
equilibrated well enough, or have a broken system, or have a temperature 
range that is too great for your integration to be stable at high T.


Mark
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[gmx-users] perl scripts to convert CHARMM ff in GROMACS

[ABEL Stephane 175950]

Hi GMXusers

I am testing the parameters of CHARMM, it works fine for lipids and protein. 
This is a great job, thanks to the devellopers But i would like to add some new 
molecule for solvent (e.g. for TFE) The atom types of TFE are present in the 
ffcharmm27bon.itp available in latest port (c32b1_release_1.1.zip, dowloaded 
http://www.dbb.su.se/User:Bjelkmar/Ffcharmm), unfortunately several bonded 
parameters (for example  F3-CF3, CF3-CT2x, etc..) are missing in 
ffcharmm27bon.itp file. So I need to convert the missing parameters into 
gromacs format. In website 
(URL:http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), I have 
found that several perl scripts exist for the conversion charmm--> gromacs. The 
archive is corrupted so, I cannot unpacked the directory to obtain the files.

Where I can find these scripts

Thanks in advance for your help

Stephane

  
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

[Chandan Choudhury]

Thanks You all.
Mark you were right. Some how mpi was screwed up. Now I am able to run the
job parallely.
Actually there were two different versions of openmpi and I suppose they
were conflicting. Uninstalling both of them and instally the recent openmpi
solved the problem

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Mon, Feb 1, 2010 at 5:02 PM, Mark Abraham wrote:

> On 01/02/10 20:19, Sarath Kumar wrote:
>
>>
>>
>>Message: 2
>>Date: Mon, 1 Feb 2010 12:31:32 +0530
>>From: Chandan Choudhury mailto:iitd...@gmail.com>>
>>
>>Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>>mpicc
>>To: Discussion list for GROMACS users >>
>>
>>Message-ID:
>><4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com
>>>
>>
>>Content-Type: text/plain; charset="iso-8859-1"
>>
>>Thanks.
>>I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
>>file, and could compile the mpi version of gromacs.
>>The next thing is I got the error on executing mdrun_mpi -h
>>Following is the output. Kindly help.
>>
>>corsica:/usr/local/gromacs/bin # mdrun_mpi -h
>>[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
>>runtime/orte_init_stage1.c at line 182
>>
>>  --
>>It looks like orte_init failed for some reason; your parallel process
>> is
>>likely to abort.  There are many reasons that a parallel process can
>>fail during orte_init; some of which are due to configuration or
>>environment problems.  This failure appears to be an internal failure;
>>here's some additional information (which may only be relevant to an
>>Open MPI developer):
>>
>>  orte_rml_base_select failed
>>  --> Returned value -13 instead of ORTE_SUCCESS
>>
>>
>>  --
>>
>>  --
>>It looks like MPI_INIT failed for some reason; your parallel process is
>>likely to abort.  There are many reasons that a parallel process can
>>fail during MPI_INIT; some of which are due to configuration or
>>environment
>>problems.  This failure appears to be an internal failure; here's some
>>additional information (which may only be relevant to an Open MPI
>>developer):
>>
>>  ompi_mpi_init: orte_init_stage1 failed
>>  --> Returned "Not found" (-13) instead of "Success" (0)
>>
>>  --
>>*** An error occurred in MPI_Init
>>*** before MPI was initialized
>>*** MPI_ERRORS_ARE_FATAL (goodbye)
>>[corsica:17130] Abort before MPI_INIT completed successfully; not
>>able to
>>guarantee that all other processes were killed!
>>
>>--
>>Chandan kumar Choudhury
>>NCL, Pune
>>INDIA
>>
>>
>>
>>
>> U will be getting error s like this
>> as the MPI failed.
>> When u run mdrun with MPI.
>>  If u use this CPPFLAGS, and i also had a problem.
>> When i used this option, after that i was unable to revert back it to
>> the original state also.
>>
>> So the better option update the gcc, c++ compilers,
>> If u have doubt in this, remove gromacs, All MPi.
>>
>> then do yum install -y *openmpi*
>>
>> --It will automatically install the missing libraries in dependencies.
>>
>> and then download fftw ---latest
>>
>> the install fftw with
>> ./configure  --enable-threads --enable-mpi
>> the gromacs
>> ./configure  --enable-threads --enable-mpi
>>
>>
>> this will surely work, because in order gromacs work with MPI.
>> U should compile fftw with MPI as above.
>>
>
> None of this will help if the MPI environment is not configured, e.g. a
> hostfile set up. Chandan needs to get a test MPI program to run before there
> is evidence any of this discussion belongs on the GROMACS mailing last.
>
> Mark
>
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[gmx-users] Re: tutorial for ionic liquid

[Vitaly V. Chaban]

> Dear all,
> Do you have any tutorial for ?
> Best regards
> Catarina

I have worked with MD of RTILs quite a lot. So if you have got
concrete questions, you can probably ask me directly.


Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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[gmx-users] Re: error: Cannot compile and link MPI code with mpicc

[Sarath Kumar]

S, I agree that MPI environment is to be configured,
this hostfile or the hosts can be defined in mpirun options.

mpirun --hostfile or mpirun --host

eg: mpirun –hostfile my_hostfile –np 4 a.out,  mpirun –host
Host1,Host2,Host3,Host4 –np 4 a.out

mpi will use the hosts of this file Which can be used after the installation
also.

I suggested the yum installation,bcoz It will resolve the mpi libraries in
the dependencies.

This hosts option is available in Lam-mpi also as Lamboot -v hostfile., then
mpirun

In MPICH2, this MPI environment can be initialized by mpdboot hostfile. then
mpirun, mpdrun

every mpi can have a hostfile to initialize it after it properly installed.
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Re: [gmx-users] non-equilibrium MD simulations

[Justin A. Lemkul]

oguz gurbulak wrote:

Dear All,
 
I'm searching for a  non-equilibrium MD tutorial done with Gromacs. 
Could you please help me to find a NEMD tutorial ?
 


"Non-equilibrium" can encompass a variety of topics, so if you want specific 
advice, you'll have to be more specific.  And, as I just mentioned to someone else:


http://lists.gromacs.org/pipermail/gmx-users/2010-February/048498.html

-Justin


Thank in advance .
 
 





--


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] non-equilibrium MD simulations

[oguz gurbulak]

Dear All,
 
I'm searching for a  non-equilibrium MD tutorial done with Gromacs. Could you 
please help me to find a NEMD tutorial ?
 
Thank in advance .
 
 


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Re: [gmx-users] tutorial for ionic liquid

[Justin A. Lemkul]

Catarina Nunes wrote:

Dear all,
Do you have any tutorial for ?
Best regards
Catarina


Gromacs tutorials can be found at:

http://www.gromacs.org/Documentation/Tutorials

If you don't find it there, try Google.  If you don't find it there, it probably 
doesn't exist :)


-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] tutorial for ionic liquid

[Catarina Nunes]

Dear all,
Do you have any tutorial for ?
Best regards
Catarina
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Re: [gmx-users] H2 topology

[David van der Spoel]

On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:

Dear all,

I want to run a simulation for an enzyme. It demands me to incorporate a
Molecular hydrogen Topology with a dummy atom in between in the
simulation in order to study the path of hydrogen in it.The problem is ,
the topology file I built induces many errors when i come to the energy
minimization step. The version of gromacs I am using is 4.0. The
topology file I built is as follows



[ moleculetype ]
;name nrexcl
H2 3

[ atoms ]
; nr type resnr residu atom cgnr charge mass ; total charge
1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
3 DUM 1 H2 DUM 1 -0.950 0.000

[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.7439756


When ever I insert the hydrogen+dummy atom topology in the protein's
.gro file, an error is generated regarding mismatch of residues or the
dummy atom having mass 0 .

I would be really grateful if anyone could provide me the hydrogen
molecule topology and give some pointers towards it.



Please print the error message in your mail.

Topology look OK, but you need to add a bond or constraint.
Also the constant probably has to be 0.5 since you want the vsite in the 
center of the two atoms.




Thank you,

Jyotsna




--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] H2 topology

[011013021-Jyotsna]

Dear all,

I want to run a simulation for an enzyme. It demands me to 
incorporate a Molecular hydrogen Topology with a dummy 
atom in between in the simulation in order to study the 
path of hydrogen in it.The problem is , the topology file 
I built induces many errors when i come to the energy 
minimization step. The version of gromacs I am using is 
4.0. The topology file I built is as follows




[ moleculetype ]
;namenrexcl
  H2   3

[ atoms ]
;   nrtype   resnr  residuatomcgnr 
  charge mass; total charge
 1 H   1 H2H1  1 
 0.4751.00800  ; 0.00
 2 H   1 H2H2  1 
 0.4751.00800  ; 0.00
 3 DUM 1 H2DUM 1 
-0.9500.000


[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.7439756


When ever I insert the hydrogen+dummy atom topology in the 
protein's .gro file, an error is generated regarding 
mismatch of residues or the dummy atom having mass 0 .


I would be really grateful if anyone could provide me the 
hydrogen molecule topology and give some pointers towards 
it.


Thank you,

Jyotsna

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Re: [gmx-users] Re : MPI

[Mark Abraham]

On 01/02/10 21:41, bharat gupta wrote:

hi all,
Can anyboddy tell me from where I can get full detail of MPI with
respect to GROMACS ..


This question is too general. Please search the GROMACS website for 
whatever you're really searching for, and if that fails, ask a focussed 
question.


Mark
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

[Mark Abraham]

On 01/02/10 20:19, Sarath Kumar wrote:



Message: 2
Date: Mon, 1 Feb 2010 12:31:32 +0530
From: Chandan Choudhury mailto:iitd...@gmail.com>>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
mpicc
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID:
<4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com
>
Content-Type: text/plain; charset="iso-8859-1"

Thanks.
I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
file, and could compile the mpi version of gromacs.
The next thing is I got the error on executing mdrun_mpi -h
Following is the output. Kindly help.

corsica:/usr/local/gromacs/bin # mdrun_mpi -h
[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_rml_base_select failed
  --> Returned value -13 instead of ORTE_SUCCESS

--
--
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or
environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: orte_init_stage1 failed
  --> Returned "Not found" (-13) instead of "Success" (0)
--
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[corsica:17130] Abort before MPI_INIT completed successfully; not
able to
guarantee that all other processes were killed!

--
Chandan kumar Choudhury
NCL, Pune
INDIA




U will be getting error s like this
as the MPI failed.
When u run mdrun with MPI.
  If u use this CPPFLAGS, and i also had a problem.
When i used this option, after that i was unable to revert back it to
the original state also.

So the better option update the gcc, c++ compilers,
If u have doubt in this, remove gromacs, All MPi.

then do yum install -y *openmpi*

--It will automatically install the missing libraries in dependencies.

and then download fftw ---latest

the install fftw with
./configure  --enable-threads --enable-mpi
the gromacs
./configure  --enable-threads --enable-mpi


this will surely work, because in order gromacs work with MPI.
U should compile fftw with MPI as above.


None of this will help if the MPI environment is not configured, e.g. a 
hostfile set up. Chandan needs to get a test MPI program to run before 
there is evidence any of this discussion belongs on the GROMACS mailing 
last.


Mark
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[gmx-users] Re : MPI

[bharat gupta]

hi all,
Can anyboddy tell me from where I can get full detail of MPI with
respect to GROMACS ..

-- 
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525
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[gmx-users] Re:J-walking REMD

[David Parcej]

gmx-users-requ...@gromacs.org wrote:

Thanks for the info Mark.

Dear All
Some time ago there was a discussion concerning the problems of REMD for
large systems and the possibility of using the REST implementation of
the method.
Mark, you mentioned that you had coded an implementation Okur method
(JCTC, 2006, 2, 420). How did it work and can you make this available?
Any other thoughts on REMD for large systems are also appreciated.



I still have my implementation, but didn't use it in anger. Reworking it 
for GROMACS 4 and using it is on my short-term to-do list.


Mark
  

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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

[Sarath Kumar]

Message: 2
> Date: Mon, 1 Feb 2010 12:31:32 +0530
> From: Chandan Choudhury 
> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>mpicc
> To: Discussion list for GROMACS users 
> Message-ID:
><4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks.
> I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
> file, and could compile the mpi version of gromacs.
> The next thing is I got the error on executing mdrun_mpi -h
> Following is the output. Kindly help.
>
> corsica:/usr/local/gromacs/bin # mdrun_mpi -h
> [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
> runtime/orte_init_stage1.c at line 182
> --
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
>
>  orte_rml_base_select failed
>  --> Returned value -13 instead of ORTE_SUCCESS
>
> --
> --
> It looks like MPI_INIT failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during MPI_INIT; some of which are due to configuration or environment
> problems.  This failure appears to be an internal failure; here's some
> additional information (which may only be relevant to an Open MPI
> developer):
>
>  ompi_mpi_init: orte_init_stage1 failed
>  --> Returned "Not found" (-13) instead of "Success" (0)
> --
> *** An error occurred in MPI_Init
> *** before MPI was initialized
> *** MPI_ERRORS_ARE_FATAL (goodbye)
> [corsica:17130] Abort before MPI_INIT completed successfully; not able to
> guarantee that all other processes were killed!
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>


U will be getting error s like this
as the MPI failed.
When u run mdrun with MPI.
 If u use this CPPFLAGS, and i also had a problem.
When i used this option, after that i was unable to revert back it to the
original state also.

So the better option update the gcc, c++ compilers,
If u have doubt in this, remove gromacs, All MPi.

then do yum install -y *openmpi*

--It will automatically install the missing libraries in dependencies.

and then download fftw ---latest

the install fftw with
./configure  --enable-threads --enable-mpi
the gromacs
./configure  --enable-threads --enable-mpi


this will surely work, because in order gromacs work with MPI.
U should compile fftw with MPI as above.

-- 
B. Sarath Kumar, B.tech.
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Re: [gmx-users] J-walking REMD

[Mark Abraham]

On 01/02/10 18:50, David van der Spoel wrote:

On 2/1/10 6:01 AM, Mark Abraham wrote:

On 27/01/10 19:00, David Parcej wrote:

Dear All
Some time ago there was a discussion concerning the problems of REMD for
large systems and the possibility of using the REST implementation of
the method.
Mark, you mentioned that you had coded an implementation Okur method
(JCTC, 2006, 2, 420). How did it work and can you make this available?
Any other thoughts on REMD for large systems are also appreciated.


I still have my implementation, but didn't use it in anger. Reworking it
for GROMACS 4 and using it is on my short-term to-do list.

Mark

Just out of curiosity what does this expression "didn't use it in anger"
mean?


Apologies, that was too idiomatic for this forum. It means I "didn't use 
it in earnest", i.e. use it thoroughly and satisfy myself that the 
implementation was working properly.


See OED entry 2a 
http://dictionary.oed.com/cgi/entry/50008418?query_type=word&queryword=anger&first=1&max_to_show=10&sort_type=alpha&result_place=1&search_id=jUhb-KYDqdW-221&hilite=50008418


Mark
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