[gmx-users] Bus error (core dumped)

[Ewaru]

Dear GROMACS experts,

I run mdrun with this command:

//mdrun -ntomp 8 -ntpi 1 -v -s em.tpr -deffnm em

After Step 67, it was terminated with a Bus error (core dumped).
Can anyone please explain this?

Thanking you in advance.





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Re: [gmx-users] Error in BlueGene

[Ricardo Soares]

Hello,

before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in
some cases even 0.5 fs. Did you tried that?

Cheers,

Ricardo.



On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote
> Mark,
> 
> Thank you for your answer.
> 
> I did an energy minimization with the file em.mdp (below) and then I 
> did a  40 ns simulation with the same md.mdp I send before. These 
> two steps were done in my local cluster. After that I took the 
> configuration for the simulation in the bluegene and I got these 
> error. I notice that the step that the error occurs depends on the 
> number of nodes I use. I am also including the end of the min.out file.
> 
> I also tried others integrators for the energy minimization but I 
> always get the same error.
> 
> Thank you again,
> Cíntia
> 
> ---
> em.mdp
> 
> integrator   = steep
> tinit= 0.0
> dt   = 0.002
> nsteps   = 500
> nstcomm  = 1
> comm-grps= Other SOL
> 
> nstxout  = 100
> nstvout  = 100
> nstfout  = 0
> nstlog   = 100
> nstenergy= 100
> nstxtcout= 100
> xtc_precision= 100
> xtc-grps =
> energygrps   = Other SOL
> 
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
> 
> coulombtype  = reaction-field
> rcoulomb = 1.4
> epsilon_rf   = 66
> 
> vdw_type = cut-off
> rvdw = 1.4
> DispCorr = No
> 
> constraints  = none
> ---
> min.out
> ...
> Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
> atom= 22015
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 5199 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -1.79302464181879e+06
> Maximum force =  6.65022934447791e+02 on atom 22015
> Norm of force =  4.90065871184878e+00
> 
> gcq#0: Thanx for Using GROMACS - Have a Nice Day
> ---
> 
> >
> >
> > ---
> > md.mdp file
> >
> >
> > integrator   = md
> > tinit= 0.0
> > dt   = 0.002
> > nsteps   = 500
> > nstcomm  = 5
> > comm-grps= Other SOL
> >
> > nstxout  = 1000
> > nstvout  = 1000
> > nstfout  = 0
> > nstlog   = 1000
> > nstenergy= 1000
> > nstxtcout= 1000
> > xtc_precision= 1000
> > xtc-grps =
> > energygrps   = Other SOL
> >
> > nstlist  = 5
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.4
> >
> > coulombtype  = reaction-field
> > rcoulomb = 1.4
> > epsilon_rf   = 66
> >
> > vdw_type = cut-off
> > rvdw = 1.4
> > DispCorr = No
> >
> > tcoupl   = v-rescale
> > tc-grps  = Other SOL
> > tau_t= 0.4 0.4
> > ref_t= 296 296
> >
> > Pcoupl   = berendsen
> > Pcoupltype   = semiisotropic
> > tau_p= 0.2 0.2
> > compressibility  = 4.51e-5 4.51e-5
> > ref_p= 1.0 1.0
> >
> > constraints  = 

[gmx-users] hi

[Kowsar Bagherzadeh]

hey have a look http://www.com-im6.net/finance/

Kowsar
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Re: [gmx-users] drug topology file

[Justin Lemkul]

On 1/30/13 3:27 PM, az kalsom wrote:

hi,

  i wanted to know, what s simple way to correct the topology generated by
PROGRG server

i have read the paper mentioned in tutorial , but still i am nt able to
correct the file

please help me, should all CH3 CH2 charge ne made zero ?



Not necessarily.  Deriving parameters for the Gromos96 force fields is a 
somewhat ill-defined process, as iterative empirical refinements are often used. 
 Building blocks of common functional groups are generally transferable between 
molecules, and recent papers have suggested parameters for many non-protein 
groups.  There are probably a dozen or so papers that I would consider necessary 
reading before you should attempt to parameterize any molecule under Gromos96.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Mark,

Thank you for your answer.

I did an energy minimization with the file em.mdp (below) and then I did 
a  40 ns simulation with the same md.mdp I send before. These two steps 
were done in my local cluster.
After that I took the configuration for the simulation in the bluegene 
and I got these error. I notice that the step that the error occurs 
depends on the number of nodes I use.

I am also including the end of the min.out file.

I also tried others integrators for the energy minimization but I always 
get the same error.


Thank you again,
Cíntia


---
em.mdp

integrator   = steep
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 1
comm-grps= Other SOL

nstxout  = 100
nstvout  = 100
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc_precision= 100
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

constraints  = none
---
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, 
atom= 22015

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.79302464181879e+06
Maximum force =  6.65022934447791e+02 on atom 22015
Norm of force =  4.90065871184878e+00

gcq#0: Thanx for Using GROMACS - Have a Nice Day
---




---
md.mdp file


integrator   = md
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 5
comm-grps= Other SOL

nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

tcoupl   = v-rescale
tc-grps  = Other SOL
tau_t= 0.4 0.4
ref_t= 296 296

Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.2 0.2
compressibility  = 4.51e-5 4.51e-5
ref_p= 1.0 1.0

constraints  = hbonds
constraint_algorithm = lincs





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Re: [gmx-users] Multiplicity of a dihedral

[Mark Abraham]

On Wed, Jan 30, 2013 at 2:17 PM, Jong Wha Lee wrote:

> Hello,
>
>
>
> How is the multiplicity of a dihedral determined? I know that it is related
> to the number of minima, but then how could we determine the number of
> minima? Is it with chemical intuition or with QM calculations?
>

Usually with intuition and whatever makes the model fit the
parameterization observables.

My molecule has several rings, which makes it not possible to calculate
> energetics when changing dihedral angles(the ring breaks). In this case,
> can
> I isolate just the four atoms (and hydrogens) and calculate energetics?
>

What are you trying to observe?

Mark
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[gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Hello,

I am having some problems to run my system in a bluegene cluster.
I am running a bilayer simulation. The simulation runs very well in my 
local cluster.


After 50ns of simulation on my local cluster with 8 nodes, I got the 
configurations and tried to run it in a bluegene with 512 nodes.
But I always get the same error (the whole output error is below as also 
the md.mdp file):

"
---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"

Can anyone help me?
Thank you,
Cíntia


---
md.mdp file


integrator   = md
tinit= 0.0
dt   = 0.002
nsteps   = 500
nstcomm  = 5
comm-grps= Other SOL

nstxout  = 1000
nstvout  = 1000
nstfout  = 0
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc-grps =
energygrps   = Other SOL

nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4

coulombtype  = reaction-field
rcoulomb = 1.4
epsilon_rf   = 66

vdw_type = cut-off
rvdw = 1.4
DispCorr = No

tcoupl   = v-rescale
tc-grps  = Other SOL
tau_t= 0.4 0.4
ref_t= 296 296

Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 0.2 0.2
compressibility  = 4.51e-5 4.51e-5
ref_p= 1.0 1.0

constraints  = hbonds
constraint_algorithm = lincs
---
error.log

vol 0.73  imb F  1% vol 0.71  imb F  1% vol 0.74  imb F  1% vol 0.74  
vol 0.74  imb F  1% vol 0.74  imb F  1% imb F  1% vol 0.75 imb F  1% vol 
0.74  imb F  1% step 3600, will finish Sat Feb  2 08:06:01 2013
Warning: 1-4 interaction between 7552 and 7556 at distance 6.386 which 
is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38174 1.38174 
1.4951


...

Step 3616  Warning: pressure scaling more than 1%, mu: 1.38219 1.38219 
1.49568
Warning: 1-4 interaction between 7556 and 7559 at distance 13.605 which 
is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 3618: Water molecule starting at atom 92582 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3618: Water molecule starting at atom 81278 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3618: Water molecule starting at atom 72206 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3618: Water molecule starting at atom 58769 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 7757 and 7762 at distance 591.859 which 
is larger than the 1-4 table size 2.400 nm
Warning: 1-4 interaction between 1301 and 1306 at distance 34172.198 
which is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 3619: Water molecule starting at atom 70238 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 3619: Water molecule starting at atom 63254 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

...

Wrote pdb files with previous and current coordinates

Step 3620:
The charge gro

Re: [gmx-users] Decreasing of the box size during membrane protein simulation

[Szilárd Páll]

Great discussion!

While (seemingly) small changes in cut-off can give considerable
performance improvements and therefore it is worth considering such tweaks
in simulation settings, these finding highlight the importance of not
changing settings blindly.

Cheers,

--
Szilárd


On Wed, Jan 30, 2013 at 2:35 PM, Justin Lemkul  wrote:

>
>
> On 1/29/13 11:57 PM, James Starlight wrote:
>
>> Justin,
>>
>>
>> with cut-offs=1.2 both in cpu+gpu or with cpu only I've obtained only
>> small decrease along the Z-dim ( from 10 to 9 nm). With cut-offs 1.0
>> I've obtained decreae from 10 to 8.5. So it might be concluded that
>> the observable is cut-off sensetive.
>>
>>
> Good to know.  Most "normal" systems of proteins in water will probably be
> insensitive to most changes with the new cutoff scheme, but I was
> suspicious about membranes.  I'll have to do some of my own testing, as
> well.
>
>
>  By the way during simulation of such system in gromos-54a7 united atom
>> ( the same number of lipids and water)  ff with 1.2 cut-offs I didnt
>> observed any decrease of the cutoffs.
>>
>>
> Different force fields behave differently.  I wouldn't expect to
> necessarily be able to draw a parallel between different parameter sets
> that inherently use different run parameters, but this is also good to know.
>
> -Justin
>
>
>  2013/1/29 Justin Lemkul :
>>
>>>
>>>
>>> On 1/29/13 2:19 AM, James Starlight wrote:
>>>

 One important point:

 in that simulations I've used decreased cut-offs with charmm36 ff
 because that systems have been modelled with CPU+GPU so I had some
 imbalance in cpu\gpu loadings with common (1.2) cutoffs.

 rlist   = 0.8   ; Cut-off for making neighbor list
 (short
 range forces)
 rlistlong   = 1.4
 rcoulomb= 0.8   ; long range electrostatic cut-off
 rvdw= 0.8


 Might that affect on the compresbility of my system? Might  I prevent
 such compression by means of changing ref_p or compressibility on the
 Z using  emiisotropic pcoupltype?


>>> Membranes are very sensitive to cutoff settings.  Can you test by
>>> running on
>>> CPU only with the normal CHARMM cutoff settings?  I would be curious to
>>> see
>>> if the shortened cutoffs produce bad results.
>>>
>>> You should not have to make any special changes to the compressibility or
>>> pressure along Z in order for the simulation to be stable.  What's
>>> happening
>>> to the x and y box vectors?  Is the membrane becoming distorted or
>>> compressed?  Or is it expanding laterally?
>>>
>>>
>>>
>>>  2013/1/29 James Starlight :

>
> Its intresting that on the same system which was equilibrated longer
> the decrease on the Z dim was smaller (from 10 to 9nm). By the way
> does it possible to simulate membrane proteins (with explicit
> membrane) in the nvt enssemble without explicit barostat ? What
> options in the mdp should be added for such simulation ?
>
>
>>> Certainly you can run in an NVT ensemble if the force field will produce
>>> good results.  Normally NPT or NPAT ensembles are most appropriate for
>>> membranes, depending on the parameterization of the lipids.  Running in
>>> NVT
>>> is as simple as setting "pcoupl = no" while leaving other
>>> thermostat-related
>>> items the same.
>>>
>>> -Justin
>>>
>>>
>>>
> James
>
> 2013/1/28 Justin Lemkul :
>
>>
>>
>>
>> On 1/28/13 8:45 AM, James Starlight wrote:
>>
>>>
>>>
>>> Justin,
>>>
>>> yes, 2 A for C atoms.
>>>
>>> The dims are 8.68740   8.41864  10.0
>>>
>>>
>> Well, with such a dramatic change, it should be fairly easy to simply
>> watch
>> the trajectory and see what went wrong.
>>
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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 listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/**Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>>>
>>> --
>>> ==**==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

[Justin Lemkul]

On 1/30/13 6:01 AM, Shima Arasteh wrote:

Dear users,

I' d like to know if I need to check the npt.gro file time by time? I mean is 
it possible for npt.gro file to reach the equilibrated state and then again 
become unequilibrated?



Unlikely, unless there's something wrong with your run parameters or topology. 
If you've done a sufficient job of equilibrating, nothing should go haywire 
unless there's something more fundamentally wrong.


-Justin



Thanks for your suggestions.
Sincerely,
Shima



From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Monday, January 28, 2013 2:32 PM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the 
same as in Trajectory

http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the
ideas that will likely help you, e.g. smaller time step, more
equilibration-friendly pressure coupling.

Mark

On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh
wrote:




It is 15 ns of NPT equilibration and I have not got a proper npt output
yet to go to the MDrun. Because when I run the -mdrun command, I get fatal
error as water molecule can not be settled.

I guess that the system might need more equilibration.

These are the settings of my npt.mdp file. The force field which I use is
C36.

integrator  = md; leap-frog integrator
nsteps  =25 ; 2 * 25 = 500 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000   ; save coordinates every 0.2 ps
nstvout = 1000   ; save velocities every 0.2 ps
nstenergy   = 1000   ; save energies every 0.2 ps
nstlog  = 1000   ; update log file every 0.2 ps

continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rlistlong   = 1.4
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
vdwtype = switch
rvdw_switch = 0.8
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover ; modified Berendsen thermostat
tc-grps = Protein POPCSOL_CL; two coupling groups - more
accurate
tau_t   = 0.5   0.5   0.5; time constant, in ps
ref_t   = 310   310   310  ; reference temperature, one for each
group, in K
pcoupl  = Parrinello-Rahman; no pressure coupling in
NVT
pcoupltype  = semiisotropic
tau_p   = 4
ref_p   = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no; account for cut-off vdW scheme
; Velocity generation
gen_vel = no   ; assign velocities from Maxwell
distribution
;gen_temp= 310   ; temperature for Maxwell distribution
;gen_seed= -1; generate a random seed
nstcomm = 1
comm_mode   = Linear
comm_grps   = Protein_POPC SOL_CL

Would you please give me any sugestions? What are the possible problems
might be considered?


Thanks for your suggestions.

Sincerely,
Shima



From: Justin Lemkul 
To: Discussion list for GROMACS users 
Sent: Sunday, January 6, 2013 9:15 AM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not
the same as in Trajectory



On 1/6/13 12:33 AM, Shima Arasteh wrote:

Do you mean that I re-run NPT step with the new index file and npt.gro

(which I got from the last NPT equilibration)? That's not clear to me yet.




That's where I'd start.  You may have to run the new configuration through
the entire equilibration protocol, though.  Instability during MD often
indicates inadequate equilibration, so whatever your protocol is may not be
sufficient as is and may require greater time.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Decreasing of the box size during membrane protein simulation

[Justin Lemkul]

On 1/29/13 11:57 PM, James Starlight wrote:

Justin,


with cut-offs=1.2 both in cpu+gpu or with cpu only I've obtained only
small decrease along the Z-dim ( from 10 to 9 nm). With cut-offs 1.0
I've obtained decreae from 10 to 8.5. So it might be concluded that
the observable is cut-off sensetive.



Good to know.  Most "normal" systems of proteins in water will probably be 
insensitive to most changes with the new cutoff scheme, but I was suspicious 
about membranes.  I'll have to do some of my own testing, as well.



By the way during simulation of such system in gromos-54a7 united atom
( the same number of lipids and water)  ff with 1.2 cut-offs I didnt
observed any decrease of the cutoffs.



Different force fields behave differently.  I wouldn't expect to necessarily be 
able to draw a parallel between different parameter sets that inherently use 
different run parameters, but this is also good to know.


-Justin


2013/1/29 Justin Lemkul :



On 1/29/13 2:19 AM, James Starlight wrote:


One important point:

in that simulations I've used decreased cut-offs with charmm36 ff
because that systems have been modelled with CPU+GPU so I had some
imbalance in cpu\gpu loadings with common (1.2) cutoffs.

rlist   = 0.8   ; Cut-off for making neighbor list (short
range forces)
rlistlong   = 1.4
rcoulomb= 0.8   ; long range electrostatic cut-off
rvdw= 0.8


Might that affect on the compresbility of my system? Might  I prevent
such compression by means of changing ref_p or compressibility on the
Z using  emiisotropic pcoupltype?



Membranes are very sensitive to cutoff settings.  Can you test by running on
CPU only with the normal CHARMM cutoff settings?  I would be curious to see
if the shortened cutoffs produce bad results.

You should not have to make any special changes to the compressibility or
pressure along Z in order for the simulation to be stable.  What's happening
to the x and y box vectors?  Is the membrane becoming distorted or
compressed?  Or is it expanding laterally?




2013/1/29 James Starlight :


Its intresting that on the same system which was equilibrated longer
the decrease on the Z dim was smaller (from 10 to 9nm). By the way
does it possible to simulate membrane proteins (with explicit
membrane) in the nvt enssemble without explicit barostat ? What
options in the mdp should be added for such simulation ?



Certainly you can run in an NVT ensemble if the force field will produce
good results.  Normally NPT or NPAT ensembles are most appropriate for
membranes, depending on the parameterization of the lipids.  Running in NVT
is as simple as setting "pcoupl = no" while leaving other thermostat-related
items the same.

-Justin




James

2013/1/28 Justin Lemkul :




On 1/28/13 8:45 AM, James Starlight wrote:



Justin,

yes, 2 A for C atoms.

The dims are 8.68740   8.41864  10.0



Well, with such a dramatic change, it should be fairly easy to simply
watch
the trajectory and see what went wrong.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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--


Justin A. Lemkul, Ph.D.
Research Scientist
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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--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Multiplicity of a dihedral

[Jong Wha Lee]

Hello,

 

How is the multiplicity of a dihedral determined? I know that it is related
to the number of minima, but then how could we determine the number of
minima? Is it with chemical intuition or with QM calculations?

My molecule has several rings, which makes it not possible to calculate
energetics when changing dihedral angles(the ring breaks). In this case, can
I isolate just the four atoms (and hydrogens) and calculate energetics?

 

Many Thanks in advance,

 

Jong Wha

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[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

[Shima Arasteh]

Dear users,

I' d like to know if I need to check the npt.gro file time by time? I mean is 
it possible for npt.gro file to reach the equilibrated state and then again 
become unequilibrated?


Thanks for your suggestions.
Sincerely,
Shima



From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Monday, January 28, 2013 2:32 PM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the 
same as in Trajectory

http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the
ideas that will likely help you, e.g. smaller time step, more
equilibration-friendly pressure coupling.

Mark

On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh
wrote:

>
>
> It is 15 ns of NPT equilibration and I have not got a proper npt output
> yet to go to the MDrun. Because when I run the -mdrun command, I get fatal
> error as water molecule can not be settled.
>
> I guess that the system might need more equilibration.
>
> These are the settings of my npt.mdp file. The force field which I use is
> C36.
>
> integrator      = md            ; leap-frog integrator
> nsteps          =25         ; 2 * 25 = 500 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 1000           ; save coordinates every 0.2 ps
> nstvout         = 1000           ; save velocities every 0.2 ps
> nstenergy       = 1000           ; save energies every 0.2 ps
> nstlog          = 1000           ; update log file every 0.2 ps
>
> continuation    = yes            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> vdwtype         = switch
> rvdw_switch     = 0.8
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
> tc-grps         = Protein POPC    SOL_CL    ; two coupling groups - more
> accurate
> tau_t           = 0.5   0.5   0.5    ; time constant, in ps
> ref_t           = 310   310   310  ; reference temperature, one for each
> group, in K
> pcoupl          = Parrinello-Rahman            ; no pressure coupling in
> NVT
> pcoupltype      = semiisotropic
> tau_p           = 4
> ref_p           = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
>
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = no    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no           ; assign velocities from Maxwell
> distribution
> ;gen_temp        = 310           ; temperature for Maxwell distribution
> ;gen_seed        = -1            ; generate a random seed
> nstcomm         = 1
> comm_mode       = Linear
> comm_grps       = Protein_POPC SOL_CL
>
> Would you please give me any sugestions? What are the possible problems
> might be considered?
>
>
> Thanks for your suggestions.
>
> Sincerely,
> Shima
>
>
> 
> From: Justin Lemkul 
> To: Discussion list for GROMACS users 
> Sent: Sunday, January 6, 2013 9:15 AM
> Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not
> the same as in Trajectory
>
>
>
> On 1/6/13 12:33 AM, Shima Arasteh wrote:
> > Do you mean that I re-run NPT step with the new index file and npt.gro
> (which I got from the last NPT equilibration)? That's not clear to me yet.
> >
>
> That's where I'd start.  You may have to run the new configuration through
> the entire equilibration protocol, though.  Instability during MD often
> indicates inadequate equilibration, so whatever your protocol is may not be
> sufficient as is and may require greater time.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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
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> * Please search the archive at
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> interface or s