date:20160623

Hi,

Yes that's pretty likely, given the lack of maintenance on this feature.

Mark

On Thu, 23 Jun 2016 23:40 Thilo Mast  wrote:

> Okay, I've found the problem.
> I think there is a problem between the communication of Gromacs v5.x and
> ORCA.
> When I use Gromacs v4.6.7 it works ...
>
>
> Am 23.06.2016 um 15:29 schrieb Thilo Mast:
> > Hi GMX users,
> >
> > I'm trying to run a QM/MM simulation with Gromacs v5.0 and ORCA v3.0.1.
> > The energy minimization of my system works! However, when I try to
> > start the MD simulation with mdrun_d -nt 1 -deffnm nvt I get the
> > following error:
> >
> > Layer 0
> > nr of QM atoms 51
> > QMlevel: RHF/3-21G*
> >
> > Setting ORCA path to: /usr/local/run/orca-3.0.1...
> > ORCA initialised...
> >
> > 1 steps,  5.0 ps.
> > Segmentation fault
> >
> > I've set the environment variables $GMX_QM_ORCA_BASENAME to "nvt" and
> > $GMX_ORCA_PATH to the path where the ORCA executable is located.
> >
> > My nvt.ORCAINFO has the following structure:
> > ! B3LYP D3BJ def2-SVP
> >
> > %method
> >  Grid2
> >  FinalGrid   4
> > end
> >
> > My nvt.mdp has the following structure:
> > integrator  = md
> > nsteps  = 1
> > dt  = 0.0005
> > ; Output control
> > nstxout = 100
> > nstvout = 100
> > nstxout-compressed = 0
> > nstenergy   = 100
> > nstlog  = 100
> > ; Bond parameters
> > continuation= no
> > constraint_algorithm= lincs
> > constraints = h-bonds
> > ; Neighborsearching
> > cutoff-scheme   = group
> > ns_type = grid
> > nstlist = 10
> > rlist= 1.2
> > rcoulomb= 1.2
> > rvdw= 1.2
> > ; Electrostatics
> > coulombtype = PME
> > ; Temperature coupling is on
> > tcoupl  = V-rescale
> > nsttcouple= 1
> > tc-grps = System
> > tau_t   = 0.1
> > ref_t   = 300
> > ; Pressure coupling is off
> > pcoupl  = no
> > ; Periodic boundary conditions
> > pbc = xyz
> > ; Dispersion correction
> > DispCorr= no
> > ; Velocity generation
> > gen_vel = yes
> > gen_temp= 300
> > gen_seed= -1
> > ; OPTIONS FOR QMMM calculations
> > QMMM = yes
> > QMMM-grps= QM
> > QMmethod = RHF; is ignored
> > QMMMscheme   = normal
> > QMbasis  = 3-21G*; is ignored
> > QMcharge = -1
> > QMmult   = 1
> >
> > Can anyone please help me?
> >
> > Best
> > Thilo
> >
>
> --
>
>
>   M. Sc. Thilo Mast
>   Karlsruhe Institute of Technology (KIT)
>   Institute of Physical Chemistry - Theoretical Chemical Biology
>   Building 30.25
>   Kaiserstr. 12
>   76131 Karlsruhe
>
>   Mail: thilo.m...@kit.edu 
>   Phone: +49 (0) 721 / 608-43572
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] Gromacs Orca QMMM segfault

2016-06-23 Thread Thilo Mast


Okay, I've found the problem.
I think there is a problem between the communication of Gromacs v5.x and 
ORCA.

When I use Gromacs v4.6.7 it works ...


Am 23.06.2016 um 15:29 schrieb Thilo Mast:

Hi GMX users,

I'm trying to run a QM/MM simulation with Gromacs v5.0 and ORCA v3.0.1.
The energy minimization of my system works! However, when I try to 
start the MD simulation with mdrun_d -nt 1 -deffnm nvt I get the 
following error:


Layer 0
nr of QM atoms 51
QMlevel: RHF/3-21G*

Setting ORCA path to: /usr/local/run/orca-3.0.1...
ORCA initialised...

1 steps,  5.0 ps.
Segmentation fault

I've set the environment variables $GMX_QM_ORCA_BASENAME to "nvt" and 
$GMX_ORCA_PATH to the path where the ORCA executable is located.


My nvt.ORCAINFO has the following structure:
! B3LYP D3BJ def2-SVP

%method
 Grid2
 FinalGrid   4
end

My nvt.mdp has the following structure:
integrator  = md
nsteps  = 1
dt  = 0.0005
; Output control
nstxout = 100
nstvout = 100
nstxout-compressed = 0
nstenergy   = 100
nstlog  = 100
; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints = h-bonds
; Neighborsearching
cutoff-scheme   = group
ns_type = grid
nstlist = 10
rlist= 1.2
rcoulomb= 1.2
rvdw= 1.2
; Electrostatics
coulombtype = PME
; Temperature coupling is on
tcoupl  = V-rescale
nsttcouple= 1
tc-grps = System
tau_t   = 0.1
ref_t   = 300
; Pressure coupling is off
pcoupl  = no
; Periodic boundary conditions
pbc = xyz
; Dispersion correction
DispCorr= no
; Velocity generation
gen_vel = yes
gen_temp= 300
gen_seed= -1
; OPTIONS FOR QMMM calculations
QMMM = yes
QMMM-grps= QM
QMmethod = RHF; is ignored
QMMMscheme   = normal
QMbasis  = 3-21G*; is ignored
QMcharge = -1
QMmult   = 1

Can anyone please help me?

Best
Thilo



--


 M. Sc. Thilo Mast
 Karlsruhe Institute of Technology (KIT)
 Institute of Physical Chemistry - Theoretical Chemical Biology
 Building 30.25
 Kaiserstr. 12
 76131 Karlsruhe

 Mail: thilo.m...@kit.edu 
 Phone: +49 (0) 721 / 608-43572

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[gmx-users] Gromacs Orca QMMM segfault

2016-06-23 Thread Thilo Mast


Hi GMX users,

I'm trying to run a QM/MM simulation with Gromacs v5.0 and ORCA v3.0.1.
The energy minimization of my system works! However, when I try to start 
the MD simulation with mdrun_d -nt 1 -deffnm nvt I get the following error:


Layer 0
nr of QM atoms 51
QMlevel: RHF/3-21G*

Setting ORCA path to: /usr/local/run/orca-3.0.1...
ORCA initialised...

1 steps,  5.0 ps.
Segmentation fault

I've set the environment variables $GMX_QM_ORCA_BASENAME to "nvt" and 
$GMX_ORCA_PATH to the path where the ORCA executable is located.


My nvt.ORCAINFO has the following structure:
! B3LYP D3BJ def2-SVP

%method
 Grid2
 FinalGrid   4
end

My nvt.mdp has the following structure:
integrator  = md
nsteps  = 1
dt  = 0.0005
; Output control
nstxout = 100
nstvout = 100
nstxout-compressed = 0
nstenergy   = 100
nstlog  = 100
; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints = h-bonds
; Neighborsearching
cutoff-scheme   = group
ns_type = grid
nstlist = 10
rlist= 1.2
rcoulomb= 1.2
rvdw= 1.2
; Electrostatics
coulombtype = PME
; Temperature coupling is on
tcoupl  = V-rescale
nsttcouple= 1
tc-grps = System
tau_t   = 0.1
ref_t   = 300
; Pressure coupling is off
pcoupl  = no
; Periodic boundary conditions
pbc = xyz
; Dispersion correction
DispCorr= no
; Velocity generation
gen_vel = yes
gen_temp= 300
gen_seed= -1
; OPTIONS FOR QMMM calculations
QMMM = yes
QMMM-grps= QM
QMmethod = RHF; is ignored
QMMMscheme   = normal
QMbasis  = 3-21G*; is ignored
QMcharge = -1
QMmult   = 1

Can anyone please help me?

Best
Thilo

--


 M. Sc. Thilo Mast
 Karlsruhe Institute of Technology (KIT)
 Institute of Physical Chemistry - Theoretical Chemical Biology
 Building 30.25
 Kaiserstr. 12
 76131 Karlsruhe

 Mail: thilo.m...@kit.edu 
 Phone: +49 (0) 721 / 608-43572

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Re: [gmx-users] How to manage carbohydrate connected to a protein




On 6/23/16 10:15 AM, Stella Maganhi wrote:

Hi Gromacs users!!!

I would like to know how to run a protein covalently bonded to a
carbohydrate in gromacs using CHARMM. The carb is covalently bonded to an
aminoacid side chain.



Use the CHARMM-GUI web interface.  It will construct the entire system and 
topology for you.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Does gmx covar/gmx anaeig give or T for ligand binding?

2016-06-23 Thread David van der Spoel


On 22/06/16 08:22, Billy Williams-Noonan wrote:

Yes, still with two ligands...  So I assume that  should be halved to
about -0.25 kJ/mol K, which would give T= -75.

I found out recently that we have access to a node with 1TB of RAM.

So the solvent is still relevant?  If the amount of memory I need for the
entropy calculation is given by *( 3*N )^2 * 4 *where N is the number of
atoms, I should be able to calculate the entropy of systems (including
solvent) on that node.  If I have to multiply by the number of frames then
I can't.

Number of frames should not be in the formula.
However including the solvent in the analysis will not help I think.
you need a PMF to get anything close to reliable.
Forget about MMPBSA.



Is the formula above correct?  Because according to it, with about 50,000
atoms in my system, I would need 90 GB of RAM, which is odd, because GMX
covar crashed when I used a node with 128GB RAM and one core.

Billy



On 22 June 2016 at 16:05, David van der Spoel  wrote:


On 22/06/16 06:44, Billy Williams-Noonan wrote:


   I re-did the calculation.  When considering the entire biomolecule of
each ensemble:

' = 51760 J/mol K

 = 50640 J/mol K

 = 814 J/mol K

   Resulting in = -0.51 kJ/mol K


Still with two ligands? This still corresponds to a binding entropy change
of -150 kJ/mol. Of course you are ignoring the entropy change of the water
which is probably almost the same magnitude and with opposite sign. If you
want more quantitative results you could consider doing a PMF but your
ligand is very large so that will be difficult to converge as well.





   And when just considering Protein-H, I got:

' = 31941 J/mol K

 = 31340 J/mol K

 = 640 J/mol K

   Resulting in = -0.69 kJ/mol K


   These values make more sense given my enthalpy calculation with
g_mmpbsa
is likely not converged.  Thank you for your time and patience. :)

Billy









On 22 June 2016 at 13:40, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

Sorry that was the ATB, not the ATP


On 22 June 2016 at 13:39, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

Hi David,


  Thanks again for responding... Sorry if I came across the wrong way.
I'm not trying to disprove the code, but simply understand why my values
don't make sense  I trust your knowledge on this subject too, since I
suspect you're one of the geniuses who helped to develop
g_covar/g_anaeig.
:)  I know the units for entropy too.

  I should explain that I have previously performed relative FEP
calculations of ligands binding to the site of interest, and reproduced
experimental binding affinities within 1.4 kcal/mol of experiment.
Ligand
topologies came from the ATP using a GROMOS united atom force-field.
So I
know that the protocol I use for system equilibration is working.

   Using the same equilibration protocol as with the FEP protocol, and
having tried an absolute FEP calculation with restraints that failed
dismally, I have a cyclic peptide that has mM affinity for the same
binding
site as the aforementioned ligands (see above paragraph).  So, using the
same protein as a model and placing the cyclic peptide in the correct
orientation as determined by the crystal structure, I am trying to use
g_mmpbsa to get an absolute binding affinity.  Of course the entropic
term
from the g_mmpbsa calculation is missing, so I am using g_covar and
g_anaeig to determine the entropy.

   You're right about the size of my ligand too of course.  The cyclic
peptide is 54 atoms in size and moves quite a lot in solution.  I am
used a
Parrinello-Rahman/V-rescale NPT ensemble, set to 300K and 1 bar, for the
entirety of the 100ns simulation.  And my protein is a symmetrical dimer
(two of the same protein bound to each other) so there is one ligand for
each monomer, forming 108 atoms between the two ligands.

   When I initially made this thread, the variables I was talking about
were:

 = 128,886 J/mol/K
= Entropy of one ligand bound to one side of the protein dimer,
despite another ligand being bound on the other side.  a_1-3071 was
selected (twice) in g covar to represent the P.L complex, despite there
being 3125 atoms in total

 = 153,548 J/mol/K
= Entropy of the protein

 = 4137 J/mol/K
= Entropy of the cyclic peptide

   So I redefined , as ', and selected a_1-3125 this
morning, to get the entropy of the dimer complexed with two cyclic
peptides, and got a value of 51,759.8 J/mol/K.  I substituted this into
the
equation (1)

 = ' -  - 2*  --(1)

   I multiplied the entropy of the ligand by two to account for the fact
that the beginning state now has the two ligands and the protein in
solution, while the end state has the protein dimer complexed with those
two ligands. And, the answer was -110.072 kJ/mol/K.

   So I am clearly doing something wrong and I'd like some advice on
what
it is...  I doubt

Re: [gmx-users] Energy minimization has stopped

Thanks a lot Justinn and Mark for the valuable suggestions.

I will start over again by choosing a force field which is suitable for the
RNA molecules.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 7:17 AM, Anurag Dobhal wrote:
>
>> Dear Justin,
>>
>> The main aim of the study is to study the interaction between a polymer
>> (chitosan) and RNA molecules by simulating them togather. I have already
>> successfully simulated my polymer system using OPLS AA force field.
>>
>> To simulate them together I need to write the OPLS AA parameters for RNA
>> molecules. I was suggested (Link Below) earlier that I can take the
>> charges
>> from any other forcefield.
>>
>> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>>
>> please enlight me where I am going wrong.
>>
>>
> I think you misunderstood what I said in that thread.
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html
>
> "You should find force field parameters specifically for the base from
> published literature or from another force field."
>
> This means: find a force field that has parametrized the species you need
> and use it.  This does not mean: hack together something from "any other
> force field" you like and try to make it OPLS-AA.  You did not say before
> that you were dealing with a complex system like this.  You just said your
> guanine charges didn't add up.  So I addressed that problem.
>
> Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an
> invalid approach.
>
> Pick a force field.  Use that force field.  Do not try to kludge together
> some hybrid entity.  Force fields are designed to be internally
> self-consistent.  If you do not have a proper balance of interactions, you
> are not doing a useful simulation.  You are generating random numbers.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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> posting!
>
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Re: [gmx-users] Energy minimization has stopped




On 6/23/16 7:17 AM, Anurag Dobhal wrote:

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.



I think you misunderstood what I said in that thread.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html

"You should find force field parameters specifically for the base from published 
literature or from another force field."


This means: find a force field that has parametrized the species you need and 
use it.  This does not mean: hack together something from "any other force 
field" you like and try to make it OPLS-AA.  You did not say before that you 
were dealing with a complex system like this.  You just said your guanine 
charges didn't add up.  So I addressed that problem.


Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an 
invalid approach.


Pick a force field.  Use that force field.  Do not try to kludge together some 
hybrid entity.  Force fields are designed to be internally self-consistent.  If 
you do not have a proper balance of interactions, you are not doing a useful 
simulation.  You are generating random numbers.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization has stopped

Hi,

You were recommended to pick a force field, not to combine parts of force
fields. Choosing to simulate your polymer OPLS/AA if you then want to
combine with RNA is not a good experimental design, unless you can do the
combined simulation also in OPLS/AA. I would repeat the polymer experiment
in whatever forcefield is also good for the experiment with RNA.

Mark

On Thu, Jun 23, 2016 at 1:18 PM Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:

> Dear Justin,
>
> The main aim of the study is to study the interaction between a polymer
> (chitosan) and RNA molecules by simulating them togather. I have already
> successfully simulated my polymer system using OPLS AA force field.
>
> To simulate them together I need to write the OPLS AA parameters for RNA
> molecules. I was suggested (Link Below) earlier that I can take the charges
> from any other forcefield.
>
> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>
> please enlight me where I am going wrong.
>
> Thank You
>
>
>
>
>
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
> *Contact: +91 8898486877*
>
>
> On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 6/23/16 7:00 AM, Anurag Dobhal wrote:
> >
> >> I am using OPLS AA force field. parameters (charges) for the atoms are
> >> taken from the charmm27 force field.
> >>
> >>
> > So, by using some hybridized force field, you can't successfully minimize
> > a structure.  That should tell you something.  Why are you trying to do
> > this, and what leads you to believe that some hybrid OPLS/CHARMM
> > combination is even sensible?  You can't just mix the charges from one
> > force field with another to create some kind of Frankenforcefield.
> >
> > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
> > optimized for RNA simulations.
> >
> > -Justin
> >
> >
> >>
> >>
> >> *Anurag Dobhal*
> >> *Graduate Student (Bioprocess Technology)*
> >> *Institute of Chemical Technology, Mumbai*
> >> *Contact: +91 8898486877*
> >>
> >>
> >>
> >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 6/23/16 6:44 AM, Justin Lemkul wrote:
> >>>
> >>>
> 
>  On 6/23/16 6:35 AM, Anurag Dobhal wrote:
> 
>  Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA
> force
> > field. I have written parameters using CHARMM27 force field for RNA
> > molecules.
> >
> >
> > What does this mean?  Are you using OPLS-AA or CHARMM27?
> 
> 
>  Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> >>> superior for RNA.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> Minimising the molecule by invoking mdrun gives me the follwoing error.
> >>>
> 
> > Energy minimization has stopped, but the forces have not converged to
> > the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size
> > was
> > too
> > small, or there was no change in the energy since last step. Either
> > way,
> > we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is
> often
> > not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> >
> >
> >
> -
> >
> > The contents of the .mdp file are the following
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> > emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> > kJ/mol/nm
> > emstep  = 0.01  ; Energy step size
> > nsteps = 5   ; Maximum number of (minimization) steps to perform
> >
> > ; Parameters describing how to find the neighbors of each atom and
> how
> > to
> > calculate the interactions
> > nstlist= 1; Frequency to update the neighbor list and long
> > range
> > forces
> > cutoff-scheme   = Verlet
> > ns_type= grid ; Method to determine neighbor list (simple, grid)
> > coulombtype= PME ; Treatment of long range electrostatic
> > interactions
> > rcoulomb= 1.0 ; Short-range electrostatic cut-off
> > rvdw= 1.0 ; Short-range Van der Waals cut-off
> > pbc= xyz ; Periodic Boundary Conditions (yes/no)
> >
> > any suggestions ?
> >
> >
> >
> 
> 
>

Re: [gmx-users] Energy minimization has stopped

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.

Thank You








*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 7:00 AM, Anurag Dobhal wrote:
>
>> I am using OPLS AA force field. parameters (charges) for the atoms are
>> taken from the charmm27 force field.
>>
>>
> So, by using some hybridized force field, you can't successfully minimize
> a structure.  That should tell you something.  Why are you trying to do
> this, and what leads you to believe that some hybrid OPLS/CHARMM
> combination is even sensible?  You can't just mix the charges from one
> force field with another to create some kind of Frankenforcefield.
>
> Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
> optimized for RNA simulations.
>
> -Justin
>
>
>>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>> *Institute of Chemical Technology, Mumbai*
>> *Contact: +91 8898486877*
>>
>>
>>
>> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>>>
>>>

 On 6/23/16 6:35 AM, Anurag Dobhal wrote:

 Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
> field. I have written parameters using CHARMM27 force field for RNA
> molecules.
>
>
> What does this mean?  Are you using OPLS-AA or CHARMM27?


 Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
>>> superior for RNA.
>>>
>>> -Justin
>>>
>>>
>>> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>

> Energy minimization has stopped, but the forces have not converged to
> the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size
> was
> too
> small, or there was no change in the energy since last step. Either
> way,
> we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often
> not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
>
>
> -
>
> The contents of the .mdp file are the following
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps = 5   ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how
> to
> calculate the interactions
> nstlist= 1; Frequency to update the neighbor list and long
> range
> forces
> cutoff-scheme   = Verlet
> ns_type= grid ; Method to determine neighbor list (simple, grid)
> coulombtype= PME ; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0 ; Short-range electrostatic cut-off
> rvdw= 1.0 ; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
> any suggestions ?
>
>
>

 http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


 mdrun prints which atom is feeling the maximum force, so that's a good
 place to
 start looking to see if there is an actual problem.

 -Justin


 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>>

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 7:00 AM, Anurag Dobhal wrote:

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.

So, by using some hybridized force field, you can't successfully minimize a
structure. That should tell you something. Why are you trying to do this, and
what leads you to believe that some hybrid OPLS/CHARMM combination is even
sensible? You can't just mix the charges from one force field with another to
create some kind of Frankenforcefield.

Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
optimized for RNA simulations.

-Justin

*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*

On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote:

On 6/23/16 6:44 AM, Justin Lemkul wrote:

On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.

What does this mean? Are you using OPLS-AA or CHARMM27?

Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly
superior for RNA.

-Justin

Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your
system).
It stopped because the algorithm tried to make a new step whose size was
too
small, or there was no change in the energy since last step. Either way,
we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often
not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 5 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

mdrun prints which atom is feeling the maximum force, so that's a good
place to
start looking to see if there is an actual problem.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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send a mail to gmx-users-requ...@gromacs.org.

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Energy minimization has stopped

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>
>>
>>
>> On 6/23/16 6:35 AM, Anurag Dobhal wrote:
>>
>>> Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
>>> field. I have written parameters using CHARMM27 force field for RNA
>>> molecules.
>>>
>>>
>> What does this mean?  Are you using OPLS-AA or CHARMM27?
>>
>>
> Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> superior for RNA.
>
> -Justin
>
>
> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>
>>> Energy minimization has stopped, but the forces have not converged to the
>>> requested precision Fmax < 1000 (which may not be possible for your
>>> system).
>>> It stopped because the algorithm tried to make a new step whose size was
>>> too
>>> small, or there was no change in the energy since last step. Either way,
>>> we
>>> regard the minimization as converged to within the available machine
>>> precision, given your starting configuration and EM parameters.
>>>
>>> Double precision normally gives you higher accuracy, but this is often
>>> not
>>> needed for preparing to run molecular dynamics.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints altogether (set constraints = none in mdp file)
>>>
>>>
>>> -
>>>
>>> The contents of the .mdp file are the following
>>>
>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>>> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
>>> kJ/mol/nm
>>> emstep  = 0.01  ; Energy step size
>>> nsteps = 5   ; Maximum number of (minimization) steps to perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to
>>> calculate the interactions
>>> nstlist= 1; Frequency to update the neighbor list and long range
>>> forces
>>> cutoff-scheme   = Verlet
>>> ns_type= grid ; Method to determine neighbor list (simple, grid)
>>> coulombtype= PME ; Treatment of long range electrostatic interactions
>>> rcoulomb= 1.0 ; Short-range electrostatic cut-off
>>> rvdw= 1.0 ; Short-range Van der Waals cut-off
>>> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>>>
>>> any suggestions ?
>>>
>>>
>>
>> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
>>
>>
>> mdrun prints which atom is feeling the maximum force, so that's a good
>> place to
>> start looking to see if there is an actual problem.
>>
>> -Justin
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>

-- 


*DISCLAIMER:*

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is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
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Re: [gmx-users] Energy minimization has stopped




On 6/23/16 6:44 AM, Justin Lemkul wrote:



On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?



Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly superior 
for RNA.


-Justin


Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-

The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?



http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


mdrun prints which atom is feeling the maximum force, so that's a good place to
start looking to see if there is an actual problem.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Energy minimization has stopped




On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?


Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-
The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?



http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

mdrun prints which atom is feeling the maximum force, so that's a good place to 
start looking to see if there is an actual problem.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Energy minimization has stopped

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.

Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-
The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?


*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*

-- 


*DISCLAIMER:*

*This communication is intended only for the person or entity to which it 
is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
necessarily reflect those of Nanomedicine Research Group.  Before opening 
the email or accessing any attachments, please check and scan for virus.*
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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi,

That depends how your mpi is implemented, but what you really want is a
filesystem visible on each node. But since mpirun gmx_mpi mdrun is working,
then it's fine.

Mark
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Re: [gmx-users] How does gromacs checkpoint works

Hi Mark,


Thank you very much!

Regards,


Husen

On Thu, Jun 23, 2016 at 3:42 PM, Mark Abraham 
wrote:

> Yes
>
> On Thu, Jun 23, 2016 at 9:54 AM Husen R  wrote:
>
> > Hi,
> >
> > Could you tell me the location of the code ?
> > is this the location of the code ->
> > gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ?
> >
> > regards,
> >
> > Husen
> >
> > On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > There's only the code. All you have to do is write down everything that
> > you
> > > were going to need to read to do the next step (unless it's from the
> > .tpr).
> > > Add some checksums of the last pieces of output files, so you can help
> > the
> > > user not mangle their files upon restart. Decide how you're going to
> > > coordinate all your ranks/cores choosing to checkpoint at the same
> time.
> > > Pick a portable file format.
> > >
> > > Mark
> > >
> > > On Thu, Jun 23, 2016 at 4:15 AM Husen R  wrote:
> > >
> > > > Hi all,
> > > >
> > > > For academic purpose, I'm wondering how does checkpoint feature in
> > > Gromacs
> > > > works ?
> > > > is there any resource/tutorial that I can learn ?
> > > >
> > > >
> > > > Thank you in advance,
> > > >
> > > >
> > > > Husen
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> or
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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi,

I'm wondering, if I use gromacs in cluster environment, do I have to
install gromacs in every nodes (at /usr/local/gromacs in every nodes) ?
or is it enough to install gromacs in one node (example,in head-node) only
?

Regards,

Husen



On Thu, Jun 23, 2016 at 3:41 PM, Mark Abraham 
wrote:

> Hi,
>
> The only explanation is that that file is not in fact properly accessible
> if rank 0 is placed other than on "compute-node," which means your
> organization of file system / slurm / etc. aren't good enough for what
> you're doing.
>
> Mark
>
> On Thu, Jun 23, 2016 at 10:15 AM Husen R  wrote:
>
> > Hi,
> >
> > I still unable to find out the cause of the fatal error.
> > Previously, gromacs is installed in every nodes. That's the cause Build
> > time mismatch and Build user mismatch appeared.
> > Now, Build time mismatch and Build user mismatch issues are solved by
> > installing Gromacs in shared directory.
> >
> > I have tried to install gromacs in one node only (not in shared
> directory),
> > but the error appeared.
> >
> >
> > this is the error message if I exclude compute-node
> > "--exclude=compute-node" from nodelist in slurm sbatch. excluding other
> > nodes works fine.
> >
> >
> >
> >
> =
> > GROMACS:  gmx mdrun, VERSION 5.1.2
> > Executable:   /mirror/source/gromacs/bin/gmx_mpi
> > Data prefix:  /mirror/source/gromacs
> > Command line:
> >   gmx_mpi mdrun -cpi md_gmx.cpt -deffnm md_gmx
> >
> >
> > Running on 2 nodes with total 8 cores, 16 logical cores
> >   Cores per node:4
> >   Logical cores per node:8
> > Hardware detected on host head-node (the node of MPI rank 0):
> >   CPU info:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
> > SIMD instructions most likely to fit this hardware: AVX_256
> > SIMD instructions selected at GROMACS compile time: AVX_256
> >
> > Reading file md_gmx.tpr, VERSION 5.1.2 (single precision)
> > Changing nstlist from 10 to 20, rlist from 1 to 1.03
> >
> >
> > Reading checkpoint file md_gmx.cpt generated: Thu Jun 23 12:54:02 2016
> >
> >
> >   #ranks mismatch,
> > current program: 16
> > checkpoint file: 24
> >
> >   #PME-ranks mismatch,
> > current program: -1
> > checkpoint file: 6
> >
> > GROMACS patchlevel, binary or parallel settings differ from previous run.
> > Continuation is exact, but not guaranteed to be binary identical.
> >
> >
> > ---
> > Program gmx mdrun, VERSION 5.1.2
> > Source code file:
> >
> /home/necis/gromacsinstall/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp,
> > line: 2216
> >
> > Fatal error:
> > Truncation of file md_gmx.xtc failed. Cannot do appending because of this
> > failure.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> 
> >
> > On Thu, Jun 16, 2016 at 6:23 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > On Thu, Jun 16, 2016 at 12:24 PM Husen R  wrote:
> > >
> > > > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > There's just nothing special about any node at run time.
> > > > >
> > > > > Your script looks like it is building GROMACS fresh each time -
> > there's
> > > > no
> > > > > need to do that,
> > > >
> > > >
> > > > which part of my script ?
> > > >
> > >
> > > I can't tell how your script is finding its GROMACS installations, but
> > the
> > > advisory message says precisely that your runs are finding different
> > > installations...
> > >
> > >   Build time mismatch,
> > > current program: Sel Apr  5 13:37:32 WIB 2016
> > > checkpoint file: Rab Apr  6 09:44:51 WIB 2016
> > >
> > >   Build user mismatch,
> > > current program: pro@head-node [CMAKE]
> > > checkpoint file: pro@compute-node [CMAKE]
> > >
> > > This reinforces my impression that the view of your file system
> available
> > > at the start of the job script is varying with your choice of node
> > subsets.
> > >
> > >
> > > > I always use this command to restart from checkpoint file -->
> "mpirun
> > > > gmx_mpi mdrun -cpi [name].cpt -deffnm [name]".
> > > > as far as I know -cpi option is used to refer to checkpoint file as
> > input
> > > > file.
> > > >  what I have to change in my script ?
> > > >
> > >
> > > Nothing about that aspect. But clearly your first run and the restart
> > > simulating loss of a node are finding different gmx_mpi binaries from
> > their
> > > respective environments. This is not itself a problem, but it's
> probably
> > > not what you intend, and may be symptomatic of the same issue that
> leads
> > to
> > >

Re: [gmx-users] How does gromacs checkpoint works

Yes

On Thu, Jun 23, 2016 at 9:54 AM Husen R  wrote:

> Hi,
>
> Could you tell me the location of the code ?
> is this the location of the code ->
> gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ?
>
> regards,
>
> Husen
>
> On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > There's only the code. All you have to do is write down everything that
> you
> > were going to need to read to do the next step (unless it's from the
> .tpr).
> > Add some checksums of the last pieces of output files, so you can help
> the
> > user not mangle their files upon restart. Decide how you're going to
> > coordinate all your ranks/cores choosing to checkpoint at the same time.
> > Pick a portable file format.
> >
> > Mark
> >
> > On Thu, Jun 23, 2016 at 4:15 AM Husen R  wrote:
> >
> > > Hi all,
> > >
> > > For academic purpose, I'm wondering how does checkpoint feature in
> > Gromacs
> > > works ?
> > > is there any resource/tutorial that I can learn ?
> > >
> > >
> > > Thank you in advance,
> > >
> > >
> > > Husen
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi,

The only explanation is that that file is not in fact properly accessible
if rank 0 is placed other than on "compute-node," which means your
organization of file system / slurm / etc. aren't good enough for what
you're doing.

Mark

On Thu, Jun 23, 2016 at 10:15 AM Husen R  wrote:

> Hi,
>
> I still unable to find out the cause of the fatal error.
> Previously, gromacs is installed in every nodes. That's the cause Build
> time mismatch and Build user mismatch appeared.
> Now, Build time mismatch and Build user mismatch issues are solved by
> installing Gromacs in shared directory.
>
> I have tried to install gromacs in one node only (not in shared directory),
> but the error appeared.
>
>
> this is the error message if I exclude compute-node
> "--exclude=compute-node" from nodelist in slurm sbatch. excluding other
> nodes works fine.
>
>
>
> =
> GROMACS:  gmx mdrun, VERSION 5.1.2
> Executable:   /mirror/source/gromacs/bin/gmx_mpi
> Data prefix:  /mirror/source/gromacs
> Command line:
>   gmx_mpi mdrun -cpi md_gmx.cpt -deffnm md_gmx
>
>
> Running on 2 nodes with total 8 cores, 16 logical cores
>   Cores per node:4
>   Logical cores per node:8
> Hardware detected on host head-node (the node of MPI rank 0):
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
> SIMD instructions most likely to fit this hardware: AVX_256
> SIMD instructions selected at GROMACS compile time: AVX_256
>
> Reading file md_gmx.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 10 to 20, rlist from 1 to 1.03
>
>
> Reading checkpoint file md_gmx.cpt generated: Thu Jun 23 12:54:02 2016
>
>
>   #ranks mismatch,
> current program: 16
> checkpoint file: 24
>
>   #PME-ranks mismatch,
> current program: -1
> checkpoint file: 6
>
> GROMACS patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
>
> ---
> Program gmx mdrun, VERSION 5.1.2
> Source code file:
> /home/necis/gromacsinstall/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp,
> line: 2216
>
> Fatal error:
> Truncation of file md_gmx.xtc failed. Cannot do appending because of this
> failure.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> 
>
> On Thu, Jun 16, 2016 at 6:23 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Thu, Jun 16, 2016 at 12:24 PM Husen R  wrote:
> >
> > > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > There's just nothing special about any node at run time.
> > > >
> > > > Your script looks like it is building GROMACS fresh each time -
> there's
> > > no
> > > > need to do that,
> > >
> > >
> > > which part of my script ?
> > >
> >
> > I can't tell how your script is finding its GROMACS installations, but
> the
> > advisory message says precisely that your runs are finding different
> > installations...
> >
> >   Build time mismatch,
> > current program: Sel Apr  5 13:37:32 WIB 2016
> > checkpoint file: Rab Apr  6 09:44:51 WIB 2016
> >
> >   Build user mismatch,
> > current program: pro@head-node [CMAKE]
> > checkpoint file: pro@compute-node [CMAKE]
> >
> > This reinforces my impression that the view of your file system available
> > at the start of the job script is varying with your choice of node
> subsets.
> >
> >
> > > I always use this command to restart from checkpoint file -->  "mpirun
> > > gmx_mpi mdrun -cpi [name].cpt -deffnm [name]".
> > > as far as I know -cpi option is used to refer to checkpoint file as
> input
> > > file.
> > >  what I have to change in my script ?
> > >
> >
> > Nothing about that aspect. But clearly your first run and the restart
> > simulating loss of a node are finding different gmx_mpi binaries from
> their
> > respective environments. This is not itself a problem, but it's probably
> > not what you intend, and may be symptomatic of the same issue that leads
> to
> > md_test.xtc not being accessible.
> >
> > Mark
> >
> >
> > >
> > > but the fact that the node name is showing up in the check
> > > > that takes place when the checkpoint is read is not relevant to the
> > > > problem.
> > > >
> > > > Mark
> > > >
> > > > On Thu, Jun 16, 2016 at 9:46 AM Husen R  wrote:
> > > >
> > > > > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <
> > > mark.j.abra...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > On Thu, Jun 16, 2016 at 9:30 AM Husen R 
> wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > >

Re: [gmx-users] restart error

2016-06-23 Thread ingram


Great thank you!

On 2016-06-23 09:39, Mark Abraham wrote:

Hi,

There's two possibilities here.

1) GROMACS has a bug with multi-simulation checkpointing - several 
people
are reporting problems, and it's probably getting an overhaul for the 
2016
release because it was far from clear the old version was always 
working


2) Your (parallel) file system isn't working well, so that output 
files
that are reported to the old run of GROMACS as being flushed to disk 
are
actually not flushed to disk, so that when the old run GROMACS reads 
the
output files "from disk" to compute the checksum it gets lied to 
again.
This information gets written into the checkpoint file. That's OK if 
the

output file really gets written to disk later on, but sometimes this
doesn't happen, particularly upon some kind of failure such as loss 
of
power. You can diagnose this by looking at the modification times of 
e.g.

your .log files. Those of the first two replicas have probably been
modified 15 minutes before all the other ones, ie at the previous
checkpointing stage. If so, complain to your system admins.

You've truncated the error message there, but you can note that 
GROMACS is
merely refusing to do appending to the old files. You can make a 
backup of
your files and re-start with mdrun -noappend, but whatever 
information

didn't get written won't be available to you for subsequent analysis.

Mark

On Thu, Jun 23, 2016 at 2:34 AM ingram  
wrote:



Dear Grommunity,

When I try and restart with the command "mpiexec -np 192 mdrun_mpi 
-v

-deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir
simann59 simann60 simann61 simann62 simann63 simann64 simann65 
simann66
simann67 simann68 simann69 simann70 simann71 simann72 simann73 
simann74"

I get the error " Fatal error: Can't read 187477 bytes of
'md_golp_vacuo.log' to compute checksum". I then see that the
simulations where this occurs are much behind the others, for 
example:


Step   Time Lambda
310031000.00.0
Step   Time Lambda
320032000.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0
Step   Time Lambda
575057500.00.0

I have already posted about this issue, and I thought I had made the
mistake. But I believe this to be a bug in GROMACS but please tell 
me if
this still seems like a user error and not GROMACS. I am using 
GROMACS

5.1.2

Best

Teresa

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Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids

2016-06-23 Thread Groenhof, Gerrit

Otherwise you may try your luck with the ATB server for Gromos topologies: 
https://atb.uq.edu.au

Gerrit

Hi,

There's a collection of contributed stuff on the GROMACS webpage, so good
luck with that... But mostly it's a matter of people choosing to share.
Authors of papers where such have been used should be willing to share
topology files.

Mark

On Thu, Jun 23, 2016 at 8:08 AM Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Hi Gromacs Users,
>
>   Does anyone know where I can find a set of download-able parameters for
> rare amino acids?  Is there a repository of some kind?
>
> Kind regards,
>
> Billy
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <
> http://www.linkedin.com/profile/preview?locale=en_US=prof-0-sb-preview-primary-button
> >
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
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End of gromacs.org_gmx-users Digest, Vol 146, Issue 128
***
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Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi,

I still unable to find out the cause of the fatal error.
Previously, gromacs is installed in every nodes. That's the cause Build
time mismatch and Build user mismatch appeared.
Now, Build time mismatch and Build user mismatch issues are solved by
installing Gromacs in shared directory.

I have tried to install gromacs in one node only (not in shared directory),
but the error appeared.


this is the error message if I exclude compute-node
"--exclude=compute-node" from nodelist in slurm sbatch. excluding other
nodes works fine.


=
GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /mirror/source/gromacs/bin/gmx_mpi
Data prefix:  /mirror/source/gromacs
Command line:
  gmx_mpi mdrun -cpi md_gmx.cpt -deffnm md_gmx


Running on 2 nodes with total 8 cores, 16 logical cores
  Cores per node:4
  Logical cores per node:8
Hardware detected on host head-node (the node of MPI rank 0):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256

Reading file md_gmx.tpr, VERSION 5.1.2 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03


Reading checkpoint file md_gmx.cpt generated: Thu Jun 23 12:54:02 2016


  #ranks mismatch,
current program: 16
checkpoint file: 24

  #PME-ranks mismatch,
current program: -1
checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.


---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/necis/gromacsinstall/gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp,
line: 2216

Fatal error:
Truncation of file md_gmx.xtc failed. Cannot do appending because of this
failure.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


On Thu, Jun 16, 2016 at 6:23 PM, Mark Abraham 
wrote:

> Hi,
>
> On Thu, Jun 16, 2016 at 12:24 PM Husen R  wrote:
>
> > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > There's just nothing special about any node at run time.
> > >
> > > Your script looks like it is building GROMACS fresh each time - there's
> > no
> > > need to do that,
> >
> >
> > which part of my script ?
> >
>
> I can't tell how your script is finding its GROMACS installations, but the
> advisory message says precisely that your runs are finding different
> installations...
>
>   Build time mismatch,
> current program: Sel Apr  5 13:37:32 WIB 2016
> checkpoint file: Rab Apr  6 09:44:51 WIB 2016
>
>   Build user mismatch,
> current program: pro@head-node [CMAKE]
> checkpoint file: pro@compute-node [CMAKE]
>
> This reinforces my impression that the view of your file system available
> at the start of the job script is varying with your choice of node subsets.
>
>
> > I always use this command to restart from checkpoint file -->  "mpirun
> > gmx_mpi mdrun -cpi [name].cpt -deffnm [name]".
> > as far as I know -cpi option is used to refer to checkpoint file as input
> > file.
> >  what I have to change in my script ?
> >
>
> Nothing about that aspect. But clearly your first run and the restart
> simulating loss of a node are finding different gmx_mpi binaries from their
> respective environments. This is not itself a problem, but it's probably
> not what you intend, and may be symptomatic of the same issue that leads to
> md_test.xtc not being accessible.
>
> Mark
>
>
> >
> > but the fact that the node name is showing up in the check
> > > that takes place when the checkpoint is read is not relevant to the
> > > problem.
> > >
> > > Mark
> > >
> > > On Thu, Jun 16, 2016 at 9:46 AM Husen R  wrote:
> > >
> > > > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > On Thu, Jun 16, 2016 at 9:30 AM Husen R  wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Thank you for your reply !
> > > > > >
> > > > > > md_test.xtc is exist and writable.
> > > > > >
> > > > >
> > > > > OK, but it needs to be seen that way from the set of compute nodes
> > you
> > > > are
> > > > > using, and organizing that is up to you and your job scheduler,
> etc.
> > > > >
> > > > >
> > > > > > I tried to restart from checkpoint file by excluding other node
> > than
> > > > > > compute-node and it works.
> > > > > >
> > > > >
> > > > > Go do that, then :-)
> > > > >
> > > >
> > > > I'm building a simple system that can respond to node failure. if
> > failure

Re: [gmx-users] selection of start or end terminus

2016-06-23 Thread Erik Marklund

Dear Alex,

A single amino acid is not a peptide sine it has no peptide bonds.

Kind regards,
Erik

> On 22 Jun 2016, at 20:19, Alexander Alexander  
> wrote:
> 
> Thanks for your response.
> 
> And then why does "1" go wrong for a single amino acid in  zwitterions
> form, as well? Isn't a single amino acid is a kind of peptide with only one
> residue?
> 
> Thanks.
> Regards,
> Alex
> 
> On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul  wrote:
> 
>> 
>> 
>> On 6/22/16 12:53 PM, Alexander Alexander wrote:
>> 
>>> Dear Gromacs user,
>>> 
>>> In the selection of start or end terminus type for peptide in OPLS_AA
>>> force
>>> field, what is the diffeece between option 0 and 1 in below list? I am
>>> interested in the Zwitterion form, but the option 0 is Zwitterion form if
>>> I
>>> am not wrong!
>>> 
>>> 
>>> Select start terminus type for 
>>> 0: NH3+
>>> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
>>> residue)
>>> 2: NH2
>>> 3: None
>>> 
>>> And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
>>> system and then the whole system in not neutral anymore but 0 is fine. It
>>> is clear below the differences and origination of the extra charge in
>>> \alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
>>> the topol file by replacing the opls_299 to opls_283 ... .?
>>> 
>>> 
>>> Choosing 0.  :-)
>>> 
>>> ; residue   1 LEU rtp LEU  q +1.0
>>>  5  opls_293B  1LEU CA  10.25 12.011
>>> 
>>> ;residue   7 GLU rtp GLU  q -2.0
>>> 112   opls_283  7GLU CA 37   0.04 12.011
>>> 
>>> 
>>> Choosing 1.   :-(
>>> 
>>> ;residue   1 LEU rtp LEU  q +0.9
>>>   5   opls_299  1LEU CA  1 0.15 12.011
>>> 
>>> ;residue   7 GLU rtp GLU  q -1.9
>>> 112   opls_299  7GLU CA 37   0.15 12.011
>>> 
>>> 
>> pdb2gmx tells you what to do:
>> 
>> "only use with zwitterions containing exactly one residue"
>> 
>> Do you have more than one residue?  If yes, this is a wrong choice.
>> 
>> -Justin
>> 
>> --
>> ==
>> 
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> ==
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Re: [gmx-users] How does gromacs checkpoint works

Hi,

Could you tell me the location of the code ?
is this the location of the code ->
gromacs-5.1.2/src/gromacs/gmxlib/checkpoint.cpp ?

regards,

Husen

On Thu, Jun 23, 2016 at 2:23 PM, Mark Abraham 
wrote:

> Hi,
>
> There's only the code. All you have to do is write down everything that you
> were going to need to read to do the next step (unless it's from the .tpr).
> Add some checksums of the last pieces of output files, so you can help the
> user not mangle their files upon restart. Decide how you're going to
> coordinate all your ranks/cores choosing to checkpoint at the same time.
> Pick a portable file format.
>
> Mark
>
> On Thu, Jun 23, 2016 at 4:15 AM Husen R  wrote:
>
> > Hi all,
> >
> > For academic purpose, I'm wondering how does checkpoint feature in
> Gromacs
> > works ?
> > is there any resource/tutorial that I can learn ?
> >
> >
> > Thank you in advance,
> >
> >
> > Husen
> > --
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Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Hi,

There's a collection of contributed stuff on the GROMACS webpage, so good
luck with that... But mostly it's a matter of people choosing to share.
Authors of papers where such have been used should be willing to share
topology files.

Mark

On Thu, Jun 23, 2016 at 8:08 AM Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Hi Gromacs Users,
>
>   Does anyone know where I can find a set of download-able parameters for
> rare amino acids?  Is there a repository of some kind?
>
> Kind regards,
>
> Billy
>
> --
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>
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> http://www.linkedin.com/profile/preview?locale=en_US=prof-0-sb-preview-primary-button
> >
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>
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Re: [gmx-users] least-squares fitting the second structure on the reference structure

Hi,

Each frame of the trajectory is fitted to the reference structure
independently of the others... but not if you're using gmx confrms, which
only acts on a single frame anyway...

Mark

On Thu, Jun 23, 2016 at 12:11 AM Qasim Pars  wrote:

> Hi Tsjerk,
>
> Thanks, I know that. I was wondering how does a second structure (for
> instance third frame) fit mathematically onto the reference structure? I
> understand the least-square fitting for only one data set but I couldn't
> understand the the least-square fitting for two data sets that fit on each
> other's.
>
> Cheers,
>
> On 23 June 2016 at 00:14, Tsjerk Wassenaar  wrote:
>
> > Hi Qasim,
> >
> > If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
> > fit onto the reference.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars 
> wrote:
> >
> > > Dear users,
> > >
> > > From GROMACS online manual:
> > > gmx confrms computes the root mean square deviation (RMSD) of two
> > > structures after least-squares fitting the second structure on the
> first
> > > one.
> > >
> > > My question is how GROMACS does least-squares fitting the second
> > structure
> > > (each frame of trajectory) on the first one (reference structure)? It
> > > calculates the least-squares fitting of the second structure and the
> > first
> > > one seperately?
> > >
> > > Thanks for your helps.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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>
>
>
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Re: [gmx-users] restart error

Hi,

There's two possibilities here.

1) GROMACS has a bug with multi-simulation checkpointing - several people
are reporting problems, and it's probably getting an overhaul for the 2016
release because it was far from clear the old version was always working

2) Your (parallel) file system isn't working well, so that output files
that are reported to the old run of GROMACS as being flushed to disk are
actually not flushed to disk, so that when the old run GROMACS reads the
output files "from disk" to compute the checksum it gets lied to again.
This information gets written into the checkpoint file. That's OK if the
output file really gets written to disk later on, but sometimes this
doesn't happen, particularly upon some kind of failure such as loss of
power. You can diagnose this by looking at the modification times of e.g.
your .log files. Those of the first two replicas have probably been
modified 15 minutes before all the other ones, ie at the previous
checkpointing stage. If so, complain to your system admins.

You've truncated the error message there, but you can note that GROMACS is
merely refusing to do appending to the old files. You can make a backup of
your files and re-start with mdrun -noappend, but whatever information
didn't get written won't be available to you for subsequent analysis.

Mark

On Thu, Jun 23, 2016 at 2:34 AM ingram  wrote:

> Dear Grommunity,
>
> When I try and restart with the command "mpiexec -np 192 mdrun_mpi -v
> -deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir
> simann59 simann60 simann61 simann62 simann63 simann64 simann65 simann66
> simann67 simann68 simann69 simann70 simann71 simann72 simann73 simann74"
> I get the error " Fatal error: Can't read 187477 bytes of
> 'md_golp_vacuo.log' to compute checksum". I then see that the
> simulations where this occurs are much behind the others, for example:
>
> Step   Time Lambda
> 310031000.00.0
> Step   Time Lambda
> 320032000.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
> Step   Time Lambda
> 575057500.00.0
>
> I have already posted about this issue, and I thought I had made the
> mistake. But I believe this to be a bug in GROMACS but please tell me if
> this still seems like a user error and not GROMACS. I am using GROMACS
> 5.1.2
>
> Best
>
> Teresa
>
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Re: [gmx-users] How does gromacs checkpoint works