date:20111010

Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Tsjerk Wassenaar

Hi Yun,

For comparison, the conditions have to be equal. That does not include
possible hardware issues. So you should be fine.

Cheers,

Tsjerk

On Oct 11, 2011 4:41 AM, "Yun Shi"  wrote:

Hi Justin,

I guess you are right, that some processors on that cluster appear to be
much slower than others.

But I am still wondering that, would the difference in initial maximum inter
charge-group distances (0.451 nm vs 0.450 nm) and minimum initial size of DD
gird (0.620nm vs 0.618nm) make the two simulations NOT comparable? Because I
want to compare the interactions of two different ligands with the same
protein.

Thanks,
Yun

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Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Mark Abraham


On 11/10/2011 1:40 PM, Yun Shi wrote:

Hi Justin,

I guess you are right, that some processors on that cluster appear to 
be much slower than others.


More likely is that the mapping of processes to processors is faulty, as 
Justin said.




But I am still wondering that, would the difference in initial maximum 
inter charge-group distances (0.451 nm vs 0.450 nm) and minimum 
initial size of DD gird (0.620nm vs 0.618nm) make the two simulations 
NOT comparable? Because I want to compare the interactions of two 
different ligands with the same protein.


That's just a detail of how the simulation is being implemented in 
parallel. There are a vast number of algorithmically equivalent ways to 
do this, and the initial conditions determine which is chosen. Since 
your initial conditions differ, so do the details.


Mark
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Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Yun Shi

Hi Justin,

I guess you are right, that some processors on that cluster appear to be
much slower than others.

But I am still wondering that, would the difference in initial maximum inter
charge-group distances (0.451 nm vs 0.450 nm) and minimum initial size of DD
gird (0.620nm vs 0.618nm) make the two simulations NOT comparable? Because I
want to compare the interactions of two different ligands with the same
protein.

Thanks,
Yun
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Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread Mark Abraham


On 11/10/2011 4:51 AM, César Ávila wrote:

v4.5.4
As I commented above, I had to manually add an entrance for the cmap 
terms in the topology file as pdb2gmx would not generate them for the 
alanine dipeptide. There seems to be no problem for larger peptides.

Cheers
Cesar



That sounds like a bug. Please describe your symptoms in a new issue 
here - http://redmine.gromacs.org 


Mark


2011/10/10 Jianguo Li mailto:ljg...@yahoo.com.sg>>

which gromacs version are you using? cMAP is implemented in v4.5 
or later

Jianguo


*From:* César Ávila mailto:clav...@gmail.com>>
*To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
*Sent:* Sunday, 9 October 2011 12:07 AM
*Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

I would like to run REMD simulations on the alanine dipeptide
using the Charmm27ff + CMAP. Still, after processing the pdb with
pdb2gmx, I do not see any entrance referring to the cmap term in
the topology file. Does this mean that Cmap won't be calculated?


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Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread Jianguo Li

After checking the topology of my peptide, I found that every term in the cMAP 
section involve three consecutive residues. So I guess no cMAP term is required 
for di-ALA. 
 
Jianguo


--- On Mon, 10/10/11, César Ávila  wrote:


From: César Ávila 
Subject: Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
To: "Jianguo Li" , "Discussion list for GROMACS users" 

Date: Monday, 10 October, 2011, 5:51 PM


v4.5.4 
As I commented above, I had to manually add an entrance for the cmap terms in 
the topology file as pdb2gmx would not generate them for the alanine dipeptide. 
There seems to be no problem for larger peptides. 
Cheers
Cesar


2011/10/10 Jianguo Li 




which gromacs version are you using? cMAP is implemented in v4.5  or later

Jianguo






From: César Ávila 
To: Discussion list for GROMACS users 
Sent: Sunday, 9 October 2011 12:07 AM
Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff



I would like to run REMD simulations on the alanine dipeptide using the 
Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see 
any entrance referring to the cmap term in the topology file. Does this mean 
that Cmap won't be calculated? 


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[gmx-users] Re: FEP

2011-10-10 Thread Fabian Casteblanco

Thanks Michael for your help.  This really helps a lot.  Thank you!

On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco
 wrote:
> Hi all,
>
> I have an additional question related to what Steven Neumann was
> mentioning.  I actually have to do a molecule mutation.  I'm trying to
> use Michael Shirts method  1) making small
> changes 'alchemical' changes in the molecules and computing the free
> energies by any method (BAR, TI, etc).  I'm specifically want to try
> to use BAR at the end once I collect all the data.  This helped a lot
> on clarification since it seemed that Justin's tutorial is essentially
> a FEP except its using the BAR mathematical method for computing the
> complete decoupling of the molecule rather than using the old FEP
> mathematics of the exponential averaging formula.  So BAR is only
> referring to the mathematical code used to calculate the overall free
> energy for the FEP, correct?
>
> My question is, for a mutation of a -CH3 group to a -H group, is it
> better to simply run:
> [+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
> --> (Lambda=1, R-CH, full charges and interactions -STATE B)]
>
> OR
>
> [1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
> 2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
> 3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
> 4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to 
> -H)
> 5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)
>
> Reason I'm asking is because when I try the first choice to do it
> STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
> the NVT equilibration right after EM, I receive errors saying that
> bonds are moving way to far off their constraints which leads me to
> believe that the system is moving too far from where it was energy
> minimized.  Errors such as:
>
> Step 188, time 0.376 (ps)
> LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.17, max 0.000636 (between atoms 9 and 68)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      9     68   31.2    0.   0.1110      0.
>
> Step 188, time 0.376 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.15, max 0.000531 (between atoms 9 and 68)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      9     68   31.0    0.   0.1110      0.
>
>
> **Please, if anybody can help, I would greatly appreciate it.  Thanks.
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Justin A. Lemkul




Yun Shi wrote:

And another difference I noticed from .log files are:
..
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808
  multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808
Minimum cell size due to bonded interactions: 0.496 nm

Optimizing the DD grid for 48 cells with a minimum initial size of 0.620 nm
The maximum allowed number of cells is: X 12 Y 12 Z 12
Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
PME domain decomposition: 8 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 21 groups of on average 2.3 processes
...

for the slow one, while for the fast one:

Initial maximum inter charge-group distances:
two-body bonded interactions: 0.450 nm, LJ-14, atoms 2064 3014
  multi-body bonded interactions: 0.450 nm, Proper Dih., atoms 2064 3014
Minimum cell size due to bonded interactions: 0.494 nm


Optimizing the DD grid for 48 cells with a minimum initial size of 0.618 nm
The maximum allowed number of cells is: X 12 Y 12 Z 12
Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
PME domain decomposition: 8 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 18 groups of on average 2.7 processes



Are these differences likely to generate huge performance difference?



I would think these differences would not account for a threefold slowdown of 
one simulation relative to the other.  Please investigate the hardware issues I 
suggested before.


-Justin

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


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Re: [gmx-users] not guaranteed to be binary identical ?

2011-10-10 Thread Justin A. Lemkul

Yun Shi wrote:

Hi all,

I am doing my MD simulations piece by piece, with -maxh and -noappend
options, so that I can link pieces of trajectories together afterward.

But as I did part0001 with 48 cores, and part0002 with 72 cores, the log
file told me that:

#nodes mismatch,
current program: 72
checkpoint file: 48

#PME-nodes mismatch,
current program: -1
checkpoint file: 16

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

I do not quite understand what it really means by "binary identical"?

Would this affect my results? In other words, would using different #
cores for each part give me different conformational assembles from
using the same # cores each part?

Several resources:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

Thanks for any help!
Yun

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

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