[gmx-users] load imbalance!!!

[delara aghaie]

Dear gromacs users
I have Dppc monolayer on Tip4p2005 water layer.
I use gromacs 4.0.7, tcoupl=v-rescale
command line in .ll file:
mpiexec mdrun -v -s topol.tpr
(I have made topol.tpr with the following command:
grompp -c .gro -f .mdp -n .ndx -p .top -o .tpr
 
now submitting the .ll file with qsub, the run has finished but I see this 
mesaage in the .e.ll file;
 
NOTE: Turning on dynamic load balancing
vol 0.69! imb F 149%
Writing final coordinates.
step 100, remaining runtime: 0 s
 Average load imbalance: 184.7 %
 Part of the total run time spent waiting due to load imbalance: 45.5 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: Z 5 %
NOTE: 45.5 % performance was lost due to load imbalance
  in the domain decomposition.
 
Is there a way to fix this load imbalance to get the better performance?
Does it mean that because of load imbalance, I have lost almost 45 percentage 
of performance?
 
Thanks in advance
Best regards
D.Aghaie-- 
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[gmx-users] 2nd question related to load imbalance

[delara aghaie]

Hello
Previously I used gromacs/3.3 for my simulations of DPPc monolayer+Tip4P2005. I 
saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load imbalance.
with this version because of load imbalance and loss of performance the 
simulation needs longer time to run.
so the question:
what is the benefit of this domain decomposition. I think it causes the runs to 
be done slower !!!.
 
thanks
D.aghaie-- 
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Re: [gmx-users] 2nd question related to load imbalance

[David van der Spoel]

On 2011-04-13 11.26, delara aghaie wrote:

Hello
Previously I used gromacs/3.3 for my simulations of DPPc
monolayer+Tip4P2005. I saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load imbalance.
with this version because of load imbalance and loss of performance the
simulation needs longer time to run.
so the question:
what is the benefit of this domain decomposition. I think it causes the
runs to be done slower !!!.
thanks
D.aghaie

4.0.7 is a lot better than 3.3 for scaling, but the latest version 4.5.4 
is even better. In addition it contains new features and bugfixes.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] 2nd question related to load imbalance

[Erik Marklund]

delara aghaie skrev 2011-04-13 11.26:

Hello
Previously I used gromacs/3.3 for my simulations of DPPc 
monolayer+Tip4P2005. I saw that it uses particle decomposition

Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load imbalance.
with this version because of load imbalance and loss of performance 
the simulation needs longer time to run.

so the question:
what is the benefit of this domain decomposition. I think it causes 
the runs to be done slower !!!.

thanks
D.aghaie

Most of the time it reduces communication of coordinates, which in turn 
can is one of the big bottlenecks in parallel MD. Domain decomposition 
makes sure that atoms which are close to eachother, and hence are likely 
to interact, are passed to the same core. With particle decomposition 
the atoms are statically asigned to the different cores, and the 
decomposition may not reflect how the aroms interact.


Why go for 4.0.7, why not 4.5.4?

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] 2nd question related to load imbalance

[delara aghaie]

Dear Dr. van der Spoel
many thanks for your explanations.
I want to know how I can overcome the performance loss due to load imbalance?
Thanks
regards
Delara
--- On Wed, 4/13/11, David van der Spoel  wrote:


From: David van der Spoel 
Subject: Re: [gmx-users] 2nd question related to load imbalance
To: "Discussion list for GROMACS users" 
Date: Wednesday, April 13, 2011, 2:01 PM


On 2011-04-13 11.26, delara aghaie wrote:
> Hello
> Previously I used gromacs/3.3 for my simulations of DPPc
> monolayer+Tip4P2005. I saw that it uses particle decomposition
> Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
> This version does the domain decomposition which causes load imbalance.
> with this version because of load imbalance and loss of performance the
> simulation needs longer time to run.
> so the question:
> what is the benefit of this domain decomposition. I think it causes the
> runs to be done slower !!!.
> thanks
> D.aghaie
> 
4.0.7 is a lot better than 3.3 for scaling, but the latest version 4.5.4 is 
even better. In addition it contains new features and bugfixes.

-- David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
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Re: [gmx-users] 2nd question related to load imbalance

[delara aghaie]

Dear Erik
Thanks for your explanation :)
regards
Delara
--- On Wed, 4/13/11, Erik Marklund  wrote:


From: Erik Marklund 
Subject: Re: [gmx-users] 2nd question related to load imbalance
To: "Discussion list for GROMACS users" 
Date: Wednesday, April 13, 2011, 2:02 PM


delara aghaie skrev 2011-04-13 11.26: 





Hello
Previously I used gromacs/3.3 for my simulations of DPPc monolayer+Tip4P2005. I 
saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load imbalance.
with this version because of load imbalance and loss of performance the 
simulation needs longer time to run.
so the question:
what is the benefit of this domain decomposition. I think it causes the runs to 
be done slower !!!.
 
thanks
D.aghaieMost of the time it reduces communication of coordinates, which in turn 
can is one of the big bottlenecks in parallel MD. Domain decomposition makes 
sure that atoms which are close to eachother, and hence are likely to interact, 
are passed to the same core. With particle decomposition the atoms are 
statically asigned to the different cores, and the decomposition may not 
reflect how the aroms interact.

Why go for 4.0.7, why not 4.5.4?

-- 
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

-Inline Attachment Follows-


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[gmx-users] mdrun_mpi!!

[delara aghaie]

Hello
In version 4.0.7 in .ll file, I use command line:
mpiexec mdrun_mpi -v -s topol.tpr
I get error which does noe recognize mdrun_mpi
I change it to mdrun and it works.
 
1) is the bold command line ok?
2) version 4.0.7 does not need _mpi after commands?
 
thanks
D.Aghaie-- 
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Re: [gmx-users] mdrun_mpi!!

[Justin A. Lemkul]

delara aghaie wrote:

Hello
In version 4.0.7 in .ll file, I use command line:
*mpiexec mdrun_mpi -v -s topol.tpr*
I get error which does noe recognize mdrun_mpi
I change it to mdrun and it works.
 
1) is the bold command line ok?


Only if you have (1) compiled with MPI support and (2) named the executable 
accordingly.



2) version 4.0.7 does not need _mpi after commands?
 


You can name the executable whatever you like, with whatever suffix you choose 
(or none at all, as the case may be).


-Justin


thanks
D.Aghaie



--


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


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[gmx-users] g_hbond error

[Chandan Choudhury]

Hello gmx-users !!

I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my systems. But the third system
should the memory problem. Below I have pasted my command and its output.

*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg -dist
hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr

No option -sel
Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision)
Specify 2 groups to analyze:
Group 0 (  System) has 95687 elements
Group 1 ( HNP) has10 elements
Group 2 (  PE) has   192 elements
Group 3 (  HP) has   216 elements
Group 4 ( CPE) has 9 elements
Group 5 ( SOL) has 95235 elements
Group 6 (  Cl) has25 elements
Group 7 ( N_H) has   126 elements
Select a group: 5
Selected 5: 'SOL'
Select a group: 7
Selected 7: 'N_H'
Checking for overlap in atoms between SOL and N_H
Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms)
Found 31795 donors and 31795 acceptors

---
Program g_hbond, VERSION 4.0.7
Source code file: smalloc.c, line: 147

Fatal error:
Not enough memory. Failed to calloc 31795 elements of size 4 for
hb->hbmap[i]
(called from file gmx_hbond.c, line 186)
---

"I Solve Problems" (Pulp Fiction)
: Cannot allocate memory
Making hbmap structure...*


Kindly help.

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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[gmx-users] Re: g_hbond error

[Chandan Choudhury]

I missed my Gromacs version. It's 4.0.7

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury wrote:

> Hello gmx-users !!
>
> I tried using g_hbond tool to analyse h-bonds on my system. I could
> successfully execute the tool for two of my systems. But the third system
> should the memory problem. Below I have pasted my command and its output.
>
> *$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg
> -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr
>
> No option -sel
> Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision)
> Specify 2 groups to analyze:
> Group 0 (  System) has 95687 elements
> Group 1 ( HNP) has10 elements
> Group 2 (  PE) has   192 elements
> Group 3 (  HP) has   216 elements
> Group 4 ( CPE) has 9 elements
> Group 5 ( SOL) has 95235 elements
> Group 6 (  Cl) has25 elements
> Group 7 ( N_H) has   126 elements
> Select a group: 5
> Selected 5: 'SOL'
> Select a group: 7
> Selected 7: 'N_H'
> Checking for overlap in atoms between SOL and N_H
> Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms)
> Found 31795 donors and 31795 acceptors
>
> ---
> Program g_hbond, VERSION 4.0.7
> Source code file: smalloc.c, line: 147
>
> Fatal error:
> Not enough memory. Failed to calloc 31795 elements of size 4 for
> hb->hbmap[i]
> (called from file gmx_hbond.c, line 186)
> ---
>
> "I Solve Problems" (Pulp Fiction)
> : Cannot allocate memory
> Making hbmap structure...*
>
>
> Kindly help.
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
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[gmx-users] Density Differences

[Kavyashree M]

Dear gromacs users,

I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
position restrained md.

integrator  = md
dt  = 0.002
nsteps  = 5
nstcomm = 10
nstlist = 5
ns_type = grid
pbc = xyz
rlist   = 1.40
coulombtype = PME
rcoulomb= 1.40
vdwtype = Switch
rvdw_switch = 0.9
rvdw= 1.00
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
Tcoupl  = nose-hoover
tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4
ref_t   = 300  300
nh-chain-length = 1
gen_vel = no
continuation= yes
constraints = all-bonds
constraint-algorithm= LINCS
lincs-order = 4
lincs-iter  = 1
lincs-warnangle = 30

when I calculate the densities, the average came out to be 1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.

Thanking you
With regards
Kavya
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RE: [gmx-users] 2nd question related to load imbalance

[Peter Lai]

You can always try mdrun -dlb yes whch will turn on dynamic load balancing from 
the beginning..

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of delara aghaie [d_agh...@yahoo.com]
Sent: Wednesday, April 13, 2011 4:41 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 2nd question related to load imbalance

Dear Dr. van der Spoel
many thanks for your explanations.
I want to know how I can overcome the performance loss due to load imbalance?
Thanks
regards
Delara
--- On Wed, 4/13/11, David van der Spoel  wrote:

From: David van der Spoel 
Subject: Re: [gmx-users] 2nd question related to load imbalance
To: "Discussion list for GROMACS users" 
Date: Wednesday, April 13, 2011, 2:01 PM

On 2011-04-13 11.26, delara aghaie wrote:
> Hello
> Previously I used gromacs/3.3 for my simulations of DPPc
> monolayer+Tip4P2005. I saw that it uses particle decomposition
> Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
> This version does the domain decomposition which causes load imbalance.
> with this version because of load imbalance and loss of performance the
> simulation needs longer time to run.
> so the question:
> what is the benefit of this domain decomposition. I think it causes the
> runs to be done slower !!!.
> thanks
> D.aghaie
>
4.0.7 is a lot better than 3.3 for scaling, but the latest version 4.5.4 is 
even better. In addition it contains new features and bugfixes.

-- David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
sp...@xray.bmc.uu.se
http://folding.bmc.uu.se
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Re: [gmx-users] Re: g_hbond error

[Erik Marklund]

Certain options require an amount of memory that is proportional to na x 
nd x t, where na and nd are number of acceptors and donors, and t is 
time. You need more memory. Or you could do your calculation for a 
subset of your solvent.


Erik

Chandan Choudhury skrev 2011-04-13 13.29:

I missed my Gromacs version. It's 4.0.7

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury > wrote:


Hello gmx-users !!

I tried using g_hbond tool to analyse h-bonds on my system. I
could successfully execute the tool for two of my systems. But the
third system should the memory problem. Below I have pasted my
command and its output.

/*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num
hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0
-xvgr
*
No option -sel
Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision)
Specify 2 groups to analyze:
Group 0 (  System) has 95687 elements
Group 1 ( HNP) has10 elements
Group 2 (  PE) has   192 elements
Group 3 (  HP) has   216 elements
Group 4 ( CPE) has 9 elements
Group 5 ( SOL) has 95235 elements
Group 6 (  Cl) has25 elements
Group 7 ( N_H) has   126 elements
Select a group: 5
Selected 5: 'SOL'
Select a group: 7
Selected 7: 'N_H'
Checking for overlap in atoms between SOL and N_H
Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126
atoms)
Found 31795 donors and 31795 acceptors

---
Program g_hbond, VERSION 4.0.7
Source code file: smalloc.c, line: 147

Fatal error:
Not enough memory. Failed to calloc 31795 elements of size 4 for
hb->hbmap[i]
(called from file gmx_hbond.c, line 186)
---

"I Solve Problems" (Pulp Fiction)
: Cannot allocate memory
Making hbmap structure.../


Kindly help.

--
Chandan kumar Choudhury
NCL, Pune
INDIA





--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] load imbalance!!!

[Mark Abraham]

On 13/04/2011 7:02 PM, delara aghaie wrote:

Dear gromacs users
I have Dppc monolayer on Tip4p2005 water layer.
I use gromacs 4.0.7, tcoupl=v-rescale
command line in .ll file:
mpiexec mdrun -v -s topol.tpr
(I have made topol.tpr with the following command:
*grompp -c .gro -f .mdp -n .ndx -p .top -o .tpr*
**
*now submitting the .ll file with qsub, the run has finished but I see 
this mesaage in the .e.ll file;*

**
NOTE: Turning on dynamic load balancing
vol 0.69! imb F 149%
Writing final coordinates.
step 100, remaining runtime: 0 s
 Average load imbalance: 184.7 %
 Part of the total run time spent waiting due to load imbalance: 45.5 %
 Steps where the load balancing was limited by -rdd, -rcon and/or 
-dds: Z 5 %

NOTE: 45.5 % performance was lost due to load imbalance
  in the domain decomposition.
Is there a way to fix this load imbalance to get the better performance?



Start using dynamic load balancing from the beginning of the run with 
-dlb yes.


Does it mean that because of load imbalance, I have lost almost 45 
percentage of performance?




Yes, but you simulated only 100 steps, so the time taken will be 
dominated by I/O and setup costs.


Some systems are intrinsically hard to treat in parallel. There's a lot 
of diagnostic data before step 0, some of which might help you 
trouble-shoot, once you demonstrate that load imbalance over a longer 
run doesn't become less significant.


Mark

Mark
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[gmx-users] Re: Problems about the simulation involving cytochrome C

[Mark Abraham]

On 13/04/2011 3:56 PM, Hui Sun wrote:

Dear sir,
I am very sorry to trouble you!


Unfortunately I am not able to act as a private tutor. Please direct 
such inquiries to the GROMACS mailing list.


Now I want to do some work about Cytochrome C using Gromos force 
field, but I don't know how to make some modifications for the force 
field to introduce chemical connectivities that are specific to this 
protein, viz., the bonds from Cys 14 and Cys 17 to the porphyrin ring 
and to hold the ligands (Met 80 and His 18) bound to the heme 
iron. See your message in the gmx-users mailling lists about the 
similar problem! 
(http://lists.gromacs.org/pipermail/gmx-users/2008-January/032039.html) I 
wonder if the problem has been solved? Could you give me more details 
about the missing parameters, such as bonds, angles and the 
corresponding force constants for bonds, angles and dihedral angles?


No. That is either months of hard work for an expert, or hours of 
literature searching if someone's already done it for a similar system. 
Please read the link I gave in that post.


Mark
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Re: [gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:

Dear gromacs users,
 
I am trying to simulate a 225aa protein at 300K in water,

with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during


You're not doing NPT.  You haven't specified pcoupl or any of the other relevant 
parameters, so you're doing NVT.



position restrained md.

integrator  = md  
dt  = 0.002
nsteps  = 5   
nstcomm = 10   
nstlist = 5  
ns_type = grid   
pbc = xyz 
rlist   = 1.40
coulombtype = PME  
rcoulomb= 1.40 
vdwtype = Switch   
rvdw_switch = 0.9  
rvdw= 1.00 
fourierspacing  = 0.12  
pme_order   = 4  
ewald_rtol  = 1e-5   
optimize_fft= yes 
Tcoupl  = nose-hoover   
tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4 
ref_t   = 300  300
nh-chain-length = 1 
gen_vel = no 
continuation= yes   
constraints = all-bonds

constraint-algorithm= LINCS
lincs-order = 4
lincs-iter  = 1   
lincs-warnangle = 30 


when I calculate the densities, the average came out to be 1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.



Simulating with the right ensemble (NPT) will equilibrate the pressure and thus 
density.  As a fundamental point, please also realize that each water model has 
its own (different) expected density value, which is also influenced somewhat by 
the remaining contents of the system.  Therefore, the result you obtain may not 
be in exact agreement with experimental bulk density of water.


-Justin


Thanking you
With regards
Kavya



--


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


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[gmx-users] Velocity distribution (a bug?)

[Mikhail Stukan]

Dear gmx-users,

I have performed further investigation on the subject  of the velocity 
distribution

http://lists.gromacs.org/pipermail/gmx-users/2011-April/060316.html

and what I found looks like a sort of a bug to me.  Namely, the velocity 
distribution profiles are different if I simulate a thermalized wall via 
dimmers with one on the particles being fixed:

[ moleculetype ]
; molname   nrexcl
  ROCK1

[ atoms ]
;id typeresnr   residu  atomcgnrcharge
1  PRC   1 ROCKPRC 1   0
2  FRC   1 ROCKFRC 2   0

[bonds]
; i j funct lengthforce.c.
  1 2 1   0.0  1000



energygrps   = FRC PRC

tcoupl   = v-rescale

tc-grps  = PRC FRC

tau_t= 0.5 0

ref_t= 300 0

freezegrps   = FRC

freezedim= Y Y Y

energygrp_excl   = FRC FRC FRC PRC PRC PRC
===

or  using position_restraints  approach:


[ moleculetype ]
; molname   nrexcl
  ROCK1

[ atoms ]
;id typeresnr   residu  atomcgnrcharge
1  PRC   1 ROCKPRC 1   0

[ position_restraints ]
; iatom type   fx  fy  fz
1  1   1 1 1
==

energygrps   = PRC
tcoupl   = v-rescale
tc-grps  = PRC
tau_t= 0.5
ref_t= 300
energygrp_excl   = PRC PRC

==

For both simulations I built the velocity distribution function using g_traj.

In both  cases the average kinetic temperature (I have calculated it from the 
averaged kinetic energy based on the velocity distributions) corresponds well 
to the one assigned to  the thermostat (300 K).

But, a) the velocity distributions for these two cases  differ from each other; 
b) neither  of them is Maxwellian.

In my simulations I use 4.5.3 version of GROMACS.

I am really lost and would very much appreciate any comments.

Many thanks in advance.
Mikhail.
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Re: [gmx-users] load imbalance!!!

[Mark Abraham]

On 13/04/2011 10:01 PM, Mark Abraham wrote:

On 13/04/2011 7:02 PM, delara aghaie wrote:

Dear gromacs users
I have Dppc monolayer on Tip4p2005 water layer.
I use gromacs 4.0.7, tcoupl=v-rescale
command line in .ll file:
mpiexec mdrun -v -s topol.tpr
(I have made topol.tpr with the following command:
*grompp -c .gro -f .mdp -n .ndx -p .top -o .tpr*
**
*now submitting the .ll file with qsub, the run has finished but I 
see this mesaage in the .e.ll file;*

**
NOTE: Turning on dynamic load balancing
vol 0.69! imb F 149%
Writing final coordinates.
step 100, remaining runtime: 0 s
 Average load imbalance: 184.7 %
 Part of the total run time spent waiting due to load imbalance: 45.5 %
 Steps where the load balancing was limited by -rdd, -rcon and/or 
-dds: Z 5 %

NOTE: 45.5 % performance was lost due to load imbalance
  in the domain decomposition.
Is there a way to fix this load imbalance to get the better performance?



Start using dynamic load balancing from the beginning of the run with 
-dlb yes.


Does it mean that because of load imbalance, I have lost almost 45 
percentage of performance?




Yes, but you simulated only 100 steps, so the time taken will be 
dominated by I/O and setup costs.


Some systems are intrinsically hard to treat in parallel. There's a 
lot of diagnostic data before step 0, some of which might help you 
trouble-shoot, once you demonstrate that load imbalance over a longer 
run doesn't become less significant.


And non-load-balanced particle decomposition will do about as well as 
dynamically load-balanced domain decomposition on moderate numbers of 
processors for fairly short simulations where particles cannot diffuse 
far. You definitely have no reason at this stage to suppose that DD is 
worse than PD for your system.


It may be that for a membrane system, customizing the domain 
decomposition to suit the inhomogeneity of the particle and interaction 
density will be necessary to get best performance early in the run. This 
is why GROMACS 3.x had grompp -sort -shuffle. GROMACS 4.x will 
eventually achieve a better load-balancing result if the simulation runs 
for long enough.


Mark
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Re: [gmx-users] Density Differences

[Kavyashree M]

I am sorry I did not include it in the mail: i used the following:

pcoupl  = Parrinello_Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0

I agree that density of water is different  depending on the model used,
so for tip4p water what is the range of fluctuations accepted? So that
we can conclude that the difference is not due to any other reason but
the water model used.

Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>  I am trying to simulate a 225aa protein at 300K in water,
>> with OPLSAA force filed, tip4p water model, using the
>> parameters below (for pressure equilibration) during
>>
>
> You're not doing NPT.  You haven't specified pcoupl or any of the other
> relevant parameters, so you're doing NVT.
>
>
>  position restrained md.
>>
>> integrator  = md  dt  =
>> 0.002nsteps  = 5   nstcomm
>>   = 10   nstlist = 5
>>  ns_type = grid   pbc = xyz
>> rlist   = 1.40
>> coulombtype = PME  rcoulomb= 1.40 vdwtype
>> = Switch   rvdw_switch = 0.9
>>  rvdw= 1.00 fourierspacing  =
>> 0.12  pme_order   = 4  ewald_rtol
>>= 1e-5   optimize_fft= yes Tcoupl
>>  = nose-hoover   tc_grps = Protein  Non-Protein
>> tau_t   = 0.4  0.4 ref_t   =
>> 300  300nh-chain-length = 1 gen_vel
>> = no continuation= yes   constraints = all-bonds
>> constraint-algorithm= LINCS
>> lincs-order = 4lincs-iter  = 1
>>   lincs-warnangle = 30
>> when I calculate the densities, the average came out to be 1025.91 kg/m^3,
>> Could anyone please clarify me the reason for this density.
>>
>>
> Simulating with the right ensemble (NPT) will equilibrate the pressure and
> thus density.  As a fundamental point, please also realize that each water
> model has its own (different) expected density value, which is also
> influenced somewhat by the remaining contents of the system.  Therefore, the
> result you obtain may not be in exact agreement with experimental bulk
> density of water.
>
> -Justin
>
>
>  Thanking you
>> With regards
>> Kavya
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before 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
>
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Re: [gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:

I am sorry I did not include it in the mail: i used the following:

pcoupl  = Parrinello_Rahman
pcoupltype  = isotropic
tau_p   = 2.0  
compressibility = 4.5e-5
ref_p   = 1.0  


I agree that density of water is different  depending on the model used,
so for tip4p water what is the range of fluctuations accepted? So that
we can conclude that the difference is not due to any other reason but
the water model used.



The extent of fluctuation in any pressure-related term depends on the size of 
your system and several of the .mdp settings.


http://www.gromacs.org/Documentation/Terminology/Pressure

For the actual target value of TIP4P density, refer to the literature.  The 
TIP4P citation is provided in the Gromacs manual.


-Justin


Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Dear gromacs users,
 I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during


You're not doing NPT.  You haven't specified pcoupl or any of the
other relevant parameters, so you're doing NVT.


position restrained md.

integrator  = md  dt
 = 0.002nsteps  = 5
  nstcomm = 10   nstlist
= 5  ns_type = grid
  pbc = xyz rlist  
= 1.40
coulombtype = PME  rcoulomb= 1.40  
  vdwtype = Switch   rvdw_switch
= 0.9  rvdw= 1.00  
  fourierspacing  = 0.12  pme_order
  = 4  ewald_rtol  = 1e-5  
optimize_fft= yes Tcoupl
 = nose-hoover   tc_grps = Protein  Non-Protein
tau_t   = 0.4  0.4 ref_t
  = 300  300nh-chain-length = 1
gen_vel = no continuation= yes  
constraints = all-bonds

constraint-algorithm= LINCS
lincs-order = 4lincs-iter  =
1   lincs-warnangle = 30
when I calculate the densities, the average came out to be
1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.


Simulating with the right ensemble (NPT) will equilibrate the
pressure and thus density.  As a fundamental point, please also
realize that each water model has its own (different) expected
density value, which is also influenced somewhat by the remaining
contents of the system.  Therefore, the result you obtain may not be
in exact agreement with experimental bulk density of water.

-Justin


Thanking you
With regards
Kavya


-- 



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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.
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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] Density Differences

[Kavyashree M]

The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?


On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> I am sorry I did not include it in the mail: i used the following:
>>
>> pcoupl  = Parrinello_Rahmanpcoupltype  =
>> isotropictau_p   = 2.0
>>  compressibility = 4.5e-5ref_p   = 1.0
>>
>> I agree that density of water is different  depending on the model used,
>> so for tip4p water what is the range of fluctuations accepted? So that
>> we can conclude that the difference is not due to any other reason but
>> the water model used.
>>
>>
> The extent of fluctuation in any pressure-related term depends on the size
> of your system and several of the .mdp settings.
>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> For the actual target value of TIP4P density, refer to the literature.  The
> TIP4P citation is provided in the Gromacs manual.
>
> -Justin
>
>  Thanking you
>> With regards
>> Kavya
>>
>> On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Kavyashree M wrote:
>>
>>Dear gromacs users,
>> I am trying to simulate a 225aa protein at 300K in water,
>>with OPLSAA force filed, tip4p water model, using the
>>parameters below (for pressure equilibration) during
>>
>>
>>You're not doing NPT.  You haven't specified pcoupl or any of the
>>other relevant parameters, so you're doing NVT.
>>
>>
>>position restrained md.
>>
>>integrator  = md  dt
>>   = 0.002nsteps  = 5
>>  nstcomm = 10   nstlist
>>= 5  ns_type = grid  pbc
>> = xyz rlist  = 1.40
>>coulombtype = PME  rcoulomb= 1.40
>>  vdwtype = Switch   rvdw_switch
>>= 0.9  rvdw= 1.00
>>  fourierspacing  = 0.12  pme_order
>>  = 4  ewald_rtol  = 1e-5
>>  optimize_fft= yes Tcoupl = nose-hoover
>>   tc_grps = Protein  Non-Protein
>>tau_t   = 0.4  0.4 ref_t
>>= 300  300nh-chain-length = 1
>>  gen_vel = no continuation= yes
>>  constraints = all-bonds
>>constraint-algorithm= LINCS
>>lincs-order = 4lincs-iter  =
>>1   lincs-warnangle = 30
>>when I calculate the densities, the average came out to be
>>1025.91 kg/m^3,
>>Could anyone please clarify me the reason for this density.
>>
>>
>>Simulating with the right ensemble (NPT) will equilibrate the
>>pressure and thus density.  As a fundamental point, please also
>>realize that each water model has its own (different) expected
>>density value, which is also influenced somewhat by the remaining
>>contents of the system.  Therefore, the result you obtain may not be
>>in exact agreement with experimental bulk density of water.
>>
>>-Justin
>>
>>
>>Thanking you
>>With regards
>>Kavya
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before 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. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the arc

Re: [gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:

The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?



That's a 2.6% difference.  I wouldn't call that "nowhere close."  Unless you are 
literally reproducing the exact same system used during parameterization (which 
you're not, based on your system contents and the use of algorithms like PME 
that didn't exist in 1983) then you shouldn't necessarily expect identical results.


-Justin



On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

I am sorry I did not include it in the mail: i used the following:

pcoupl  = Parrinello_Rahmanpcoupltype  
   = isotropictau_p   = 2.0
 compressibility = 4.5e-5ref_p  
= 1.0  
I agree that density of water is different  depending on the

model used,
so for tip4p water what is the range of fluctuations accepted?
So that
we can conclude that the difference is not due to any other
reason but
the water model used.


The extent of fluctuation in any pressure-related term depends on
the size of your system and several of the .mdp settings.

http://www.gromacs.org/Documentation/Terminology/Pressure

For the actual target value of TIP4P density, refer to the
literature.  The TIP4P citation is provided in the Gromacs manual.

-Justin

Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Kavyashree M wrote:

   Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
   with OPLSAA force filed, tip4p water model, using the
   parameters below (for pressure equilibration) during


   You're not doing NPT.  You haven't specified pcoupl or any of the
   other relevant parameters, so you're doing NVT.


   position restrained md.

   integrator  = md  dt
= 0.002nsteps  
   = 5  nstcomm = 10
  nstlist= 5
 ns_type = grid  pbc
= xyz rlist  = 1.40

   coulombtype = PME  rcoulomb=
1.40vdwtype = Switch  
rvdw_switch= 0.9  rvdw  
 = 1.00fourierspacing  =
0.12  pme_order  = 4
 ewald_rtol  = 1e-5
 optimize_fft= yes Tcoupl =

nose-hoover   tc_grps = Protein  Non-Protein
   tau_t   = 0.4  0.4 ref_t
 = 300  300nh-chain-length  
  = 1gen_vel = no continuation  
 = yes  constraints = all-bonds

   constraint-algorithm= LINCS
   lincs-order = 4lincs-iter
 =

   1   lincs-warnangle = 30
   when I calculate the densities, the average came out to be
   1025.91 kg/m^3,
   Could anyone please clarify me the reason for this density.


   Simulating with the right ensemble (NPT) will equilibrate the
   pressure and thus density.  As a fundamental point, please also
   realize that each water model has its own (different) expected
   density value, which is also influenced somewhat by the remaining
   contents of the system.  Therefore, the result you obtain may
not be
   in exact agreement with experimental bulk density of water.

   -Justin


   Thanking you
   With regards
   Kavya


   -- 

   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

   ===

Re: [gmx-users] Density Differences

[Kavyashree M]

Ok Thanks.

On Wed, Apr 13, 2011 at 6:22 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
>> stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
>> close to the value i have got. (1.025g/cc). or is this value tolerable?
>>
>>
> That's a 2.6% difference.  I wouldn't call that "nowhere close."  Unless
> you are literally reproducing the exact same system used during
> parameterization (which you're not, based on your system contents and the
> use of algorithms like PME that didn't exist in 1983) then you shouldn't
> necessarily expect identical results.
>
> -Justin
>
>
>> On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Kavyashree M wrote:
>>
>>I am sorry I did not include it in the mail: i used the following:
>>
>>pcoupl  = Parrinello_Rahmanpcoupltype
>>   = isotropictau_p   = 2.0
>>   compressibility = 4.5e-5ref_p
>>  = 1.0  I agree that density of water is
>> different  depending on the
>>model used,
>>so for tip4p water what is the range of fluctuations accepted?
>>So that
>>we can conclude that the difference is not due to any other
>>reason but
>>the water model used.
>>
>>
>>The extent of fluctuation in any pressure-related term depends on
>>the size of your system and several of the .mdp settings.
>>
>>http://www.gromacs.org/Documentation/Terminology/Pressure
>>
>>For the actual target value of TIP4P density, refer to the
>>literature.  The TIP4P citation is provided in the Gromacs manual.
>>
>>-Justin
>>
>>Thanking you
>>With regards
>>Kavya
>>
>>On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Kavyashree M wrote:
>>
>>   Dear gromacs users,
>>I am trying to simulate a 225aa protein at 300K in water,
>>   with OPLSAA force filed, tip4p water model, using the
>>   parameters below (for pressure equilibration) during
>>
>>
>>   You're not doing NPT.  You haven't specified pcoupl or any of
>> the
>>   other relevant parameters, so you're doing NVT.
>>
>>
>>   position restrained md.
>>
>>   integrator  = md  dt
>>= 0.002nsteps
>> = 5  nstcomm = 10
>>  nstlist= 5 ns_type
>> = grid  pbc= xyz
>> rlist  = 1.40
>>   coulombtype = PME  rcoulomb=
>>1.40vdwtype = Switch
>>  rvdw_switch= 0.9  rvdw
>>   = 1.00fourierspacing  =
>>0.12  pme_order  = 4
>>   ewald_rtol  = 1e-5
>> optimize_fft= yes Tcoupl =
>>nose-hoover   tc_grps = Protein  Non-Protein
>>   tau_t   = 0.4  0.4 ref_t
>> = 300  300nh-chain-length
>>  = 1gen_vel = no continuation
>> = yes  constraints = all-bonds
>>   constraint-algorithm= LINCS
>>   lincs-order = 4lincs-iter
>>   =
>>   1   lincs-warnangle = 30
>>   when I calculate the densities, the average came out to be
>>   1025.91 kg/m^3,
>>   Could anyone please clarify me the reason for this density.
>>
>>
>>   Simulating with the right ensemble (NPT) will equilibrate the
>>   pressure and thus density.  As a fundamental point, please also
>>   realize that each water model has its own (different) expected
>>   density value, which is also influenced somewhat by the
>> remaining
>>   contents of the system.  Therefore, the result you obtain may
>>not be
>>   in exact agreement with experimental bulk density of water.
>>
>>   -Justin
>>
>>
>>   Thanking you
>>   With regards
>>   Kavya
>>
>>
>>   -- 
>>
>>   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
>>
>>   htt

[gmx-users] create a sphere of water molecules

[Olga Ivchenko]

Dear Gromacs Users,

I want to add a sphere of water molecules around a ligand. I know I need to
use -shell option in genbox. But first I I need to create a sphere. Please
could you guide me?

best,
Olga
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[gmx-users] amide partial charges in G56A3

[XUEMING TANG]

Hi there

The amide partial charges in the share folder of gromacs G56A3ff is as
following
   H H: +0.280  N: -0.280
|  C: -0.380   O: -0.380
C-N-C-C  other C : 0.000
   "
   O

I guess all protein people use partial charges of amide like above because
it is in the forcefield file? I am wondering where are those numbers come
from? Any reference will be great!
(I know in Justin Lemkul 2010 paper he discusses about the partial charges
of amide. I am curious about how gromacs sign those numbers. It must be good
although different form gaussian calculations.)

Thank you for your time!

Cheers!
Xueming
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Re: [gmx-users] amide partial charges in G56A3

[Justin A. Lemkul]

XUEMING TANG wrote:

Hi there

The amide partial charges in the share folder of gromacs G56A3ff is as 
following

   H H: +0.280  N: -0.280
|  C: -0.380   O: -0.380
C-N-C-C  other C : 0.000
   "
   O

I guess all protein people use partial charges of amide like above 
because it is in the forcefield file? I am wondering where are those 
numbers come from? Any reference will be great!


Anyone who uses this particular parameter set will use these partial charges, 
yes.

http://dx.doi.org/10.1002/jcc.20090

(I know in Justin Lemkul 2010 paper he discusses about the partial 
charges of amide. I am curious about how gromacs sign those numbers. It 
must be good although different form gaussian calculations.)




Gromos96 parameterization uses empirical adjustment to reproduce condensed-phase 
behavior and thermodynamic properties (see paper linked above), thus most QM 
calculations will not reproduce these partial charges, as we demonstrated in 
that work.


-Justin


Thank you for your time!

Cheers!
Xueming



--


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] create a sphere of water molecules

[Erik Marklund]

Olga Ivchenko skrev 2011-04-13 15.20:



Dear Gromacs Users,

I want to add a sphere of water molecules around a ligand. I know I 
need to use -shell option in genbox. But first I I need to create a 
sphere. Please could you guide me?


best,
Olga
Just fill the box with water, then run trjorder to sort the solvent 
according to their distance to the ligand. Having done that, you can 
just edit away the bottom part of the sorted gro-file to have your 
ligand in a ball of water.


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] create a sphere of water molecules

[Esteban Gabriel Vega Hissi]

Hi,

You can try "packmol" (
http://www.ime.unicamp.br/~martinez/packmol/download.html) to create any
starting configuration of your interest. I found it very useful for random
initial configurations.

Hope this help.


Esteban Gabriel Vega Hissi
Área de Química Física
Departamento de Química
Universidad Nacional de San Luis
Argentina

On Wed, Apr 13, 2011 at 10:48 AM, Erik Marklund wrote:

> Olga Ivchenko skrev 2011-04-13 15.20:
>
>
>>
>> Dear Gromacs Users,
>>
>> I want to add a sphere of water molecules around a ligand. I know I need
>> to use -shell option in genbox. But first I I need to create a sphere.
>> Please could you guide me?
>>
>> best,
>> Olga
>>
> Just fill the box with water, then run trjorder to sort the solvent
> according to their distance to the ligand. Having done that, you can just
> edit away the bottom part of the sorted gro-file to have your ligand in a
> ball of water.
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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>
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[gmx-users] make a patch

[Nilesh Dhumal]

Hello,

I want to file a patch for g_hbond.

How can I do that.

Nilesh




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Re: [gmx-users] make a patch

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

I want to file a patch for g_hbond.

How can I do that.


Post a feature/enhancement request on redmine.gromacs.org.

-Justin



Nilesh






--


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] RE: How to install GROMACS in Rocks Cluster 5.4 :ERROR

[christopher . yip]

Sent from my BlackBerry® wireless device

-Original Message-
From:   Mark Abraham 
Sender: gmx-users-boun...@gromacs.org
Date:   Wed, 13 Apr 2011 07:35:30 
To: Discussion list for GROMACS users
Reply-To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 :
ERROR

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Re: [gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 :ERROR

[christopher . yip]

Sent from my BlackBerry® wireless device

-Original Message-
From:   Mark Abraham 
Sender: gmx-users-boun...@gromacs.org
Date:   Wed, 13 Apr 2011 07:35:30 
To: Discussion list for GROMACS users
Reply-To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 :
ERROR

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[gmx-users] pulling of a metal

[Jon Mujika]

Dear all,

I am trying to pull a metal out of the protein binding pocket following a
cavity in the protein structure. I followed the tutorial, but I find few
problems:

1) When the metal leaves the binding pocket, some ligands "follow" the
metal, even that  I restrained the position of protein atoms (force constant
of 1000 or 3000). I would like to keep the protein as it is.

2) The metal does not leave the protein through the cavity. How can I define
this? I can take a water molecule in the cavity as reference, but I do not
how to deal with this.

This is the pull section in the mdp file:

pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = Metal
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 3000  ; kJ mol^-1 nm^-2

Thanks in advance for your help

Jon Mujika
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Re: [gmx-users] pulling of a metal

[Justin A. Lemkul]

Jon Mujika wrote:

Dear all,

I am trying to pull a metal out of the protein binding pocket following 
a cavity in the protein structure. I followed the tutorial, but I find 
few problems:


1) When the metal leaves the binding pocket, some ligands "follow" the 
metal, even that  I restrained the position of protein atoms (force 
constant of 1000 or 3000). I would like to keep the protein as it is.




Use stronger restraints and/or freezegrps.

2) The metal does not leave the protein through the cavity. How can I 
define this? I can take a water molecule in the cavity as reference, but 
I do not how to deal with this.




Pull along a defined vector, i.e. pull_vec1.  You can use a water molecule that 
is initially in the desired cavity to easily calculate this vector.


-Justin


This is the pull section in the mdp file:

pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = Metal
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 3000  ; kJ mol^-1 nm^-2

Thanks in advance for your help

Jon Mujika



--


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


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[gmx-users] compression- NPT

[Moeed]

Hello everyone,

I have encountered a strange behavior while compressing a pure system.

I am applying 100 bar pressure with PME and it turned out that this pressure
leads to density of 20 SI. Changing PME to SHIFT compresses the system to
density of above 600 SI!! and I should add that PME and shift on my system
give essentially identical results ( I mean all those properties listed in
g_energy)

Also, when I take a configuration from a run which is compressed to a higher
density which is still off the desired density, applying a even higher
pressure in the next run not only does not leads to further compression but
causes the box expand to a much bigger size!

How can this be justified?

Thanks for your suggestions,
moeed
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[gmx-users] Regarding g_enemat

[bipin singh]

Hello,

I am using g_enemat to calculate the energy matrix from the energy
file(edr file) and I am supplying Protein as a group in -groups
option.
The command I am supplied is as follows:

g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
energy.xvg -temp 328 -nocoul -nolj -nomean

but I am getting the following error
Read 1 groups
group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy file

As written in the manual:
"Energy groups with names like ’Coul-SR:Protein-SOL’ and
’LJ:Protein-SOL’ are expected in the energy
file"
But I am not clear how to get these terms in energy file.

The energy file I am supplying is from a 100 ns md simulation.

-- 
---
Regards,
Bipin Singh
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Re: [gmx-users] Regarding g_enemat

[Justin A. Lemkul]

bipin singh wrote:

Hello,

I am using g_enemat to calculate the energy matrix from the energy
file(edr file) and I am supplying Protein as a group in -groups
option.
The command I am supplied is as follows:

g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
energy.xvg -temp 328 -nocoul -nolj -nomean

but I am getting the following error
Read 1 groups
group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy file

As written in the manual:
"Energy groups with names like ’Coul-SR:Protein-SOL’ and
’LJ:Protein-SOL’ are expected in the energy
file"
But I am not clear how to get these terms in energy file.



Whatever name you supply has to be an actual term in the .edr file.  Run 
g_energy first to get a list of all valid energy terms if you are unfamiliar 
with the contents of the .edr file.


-Justin


The energy file I am supplying is from a 100 ns md simulation.



--


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] Regarding g_enemat

[bipin singh]

Thanks for your reply

The following terms are present in my energy files

1  Angle2  Proper-Dih.  3  Improper-Dih.4  LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  Disper.-corr.8  Coulomb-(SR)
  9  Coul.-recip.10  Potential   11  Kinetic-En. 12  Total-Energy
 13  Temperature 14  Pres.-DC15  Pressure16  Constr.-rmsd
 17  Box-X   18  Box-Y   19  Box-Z   20  Volume
 21  Density 22  pV23  Enthalpy24
Vir-XX
 25  Vir-XY  26  Vir-XZ27  Vir-YX  28
Vir-YY
 29  Vir-YZ  30  Vir-ZX 31  Vir-ZY  32
Vir-ZZ
 33  Pres-XX 34  Pres-XY 35  Pres-XZ 36  Pres-YX
 37  Pres-YY 38  Pres-YZ 39  Pres-ZX 40  Pres-ZY
 41  Pres-ZZ 42  #Surf*SurfTen  43  Box-Vel-XX  44  Box-Vel-YY
 45  Box-Vel-ZZ  46  Mu-X47  Mu-Y48  Mu-Z
 49  T-Protein  50  T-non-Protein
 51  Lamb-Protein   52  Lamb-non-Protein

So, please suggest why I am getting error, If the LJ-(SR) and Coulomb-(SR)
terms are already present in the energy file.

On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul  wrote:
>
>
> bipin singh wrote:
>>
>> Hello,
>>
>> I am using g_enemat to calculate the energy matrix from the energy
>> file(edr file) and I am supplying Protein as a group in -groups
>> option.
>> The command I am supplied is as follows:
>>
>> g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
>> energy.xvg -temp 328 -nocoul -nolj -nomean
>>
>> but I am getting the following error
>> Read 1 groups
>> group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy
>> file
>>
>> As written in the manual:
>> "Energy groups with names like ’Coul-SR:Protein-SOL’ and
>> ’LJ:Protein-SOL’ are expected in the energy
>> file"
>> But I am not clear how to get these terms in energy file.
>>
>
> Whatever name you supply has to be an actual term in the .edr file.  Run
> g_energy first to get a list of all valid energy terms if you are unfamiliar
> with the contents of the .edr file.
>
> -Justin
>
>> The energy file I am supplying is from a 100 ns md simulation.
>>
>
> --
> 
>
> 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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Regards,
Bipin Singh
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Re: [gmx-users] Regarding g_enemat

[Justin A. Lemkul]

bipin singh wrote:

Thanks for your reply

The following terms are present in my energy files

1  Angle2  Proper-Dih.  3  Improper-Dih.4  LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  Disper.-corr.8  Coulomb-(SR)
  9  Coul.-recip.10  Potential   11  Kinetic-En. 12  Total-Energy
 13  Temperature 14  Pres.-DC15  Pressure16  Constr.-rmsd
 17  Box-X   18  Box-Y   19  Box-Z   20  Volume
 21  Density 22  pV23  Enthalpy24
Vir-XX
 25  Vir-XY  26  Vir-XZ27  Vir-YX  28
Vir-YY
 29  Vir-YZ  30  Vir-ZX 31  Vir-ZY  32
Vir-ZZ
 33  Pres-XX 34  Pres-XY 35  Pres-XZ 36  Pres-YX
 37  Pres-YY 38  Pres-YZ 39  Pres-ZX 40  Pres-ZY
 41  Pres-ZZ 42  #Surf*SurfTen  43  Box-Vel-XX  44  Box-Vel-YY
 45  Box-Vel-ZZ  46  Mu-X47  Mu-Y48  Mu-Z
 49  T-Protein  50  T-non-Protein
 51  Lamb-Protein   52  Lamb-non-Protein

So, please suggest why I am getting error, If the LJ-(SR) and Coulomb-(SR)
terms are already present in the energy file.



Please read the g_enemat help description again and refer to the example 
groups.dat file it provides.  You haven't set any energrygrps (in the .mdp file, 
for which certain terms are decomposed and stored in the .edr file) that 
g_enemat can act upon.  Every term listed here is simply for the entire system.


-Justin


On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul  wrote:


bipin singh wrote:

Hello,

I am using g_enemat to calculate the energy matrix from the energy
file(edr file) and I am supplying Protein as a group in -groups
option.
The command I am supplied is as follows:

g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
energy.xvg -temp 328 -nocoul -nolj -nomean

but I am getting the following error
Read 1 groups
group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy
file

As written in the manual:
"Energy groups with names like ’Coul-SR:Protein-SOL’ and
’LJ:Protein-SOL’ are expected in the energy
file"
But I am not clear how to get these terms in energy file.


Whatever name you supply has to be an actual term in the .edr file.  Run
g_energy first to get a list of all valid energy terms if you are unfamiliar
with the contents of the .edr file.

-Justin


The energy file I am supplying is from a 100 ns md simulation.


--


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


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[gmx-users] OPLS with Water models

[Jianhui Tian]

Hi,

This has been a long discussed question. But I am still not so clear after
reading some posts and papers.
What model should be used for OPLS-AA force field? Any consideration for the
choice? Is SPC/E a good one?

Michael shirts has said in
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html
"Jorgensen's OPLS-AA (and more recent OPLS-AA/L) force fields were developed
almost completely with TIP4P water. "
Also, David van der spoel had a paper with  Erik Lindahl (JPCB 2003, 117,
11178-11187) confirming: "OPLS works better with TIP4P".

However, many simulations using OPLS with SPC or TIP3P.

Alan Wilter S. da Silva said in
http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.html that

"I did short tests with spce and I got a paper with Dr. der Spoel."
But I can not find any paper for OPLS-AA and SPC/E water.

Suggestions or references are welcomed.
Thanks.

Jianhui
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Re: [gmx-users] OPLS with Water models

[Justin A. Lemkul]

Jianhui Tian wrote:

Hi,

This has been a long discussed question. But I am still not so clear 
after reading some posts and papers.
What model should be used for OPLS-AA force field? Any consideration for 
the choice? Is SPC/E a good one?


Michael shirts has said in 
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html
"Jorgensen's OPLS-AA (and more recent OPLS-AA/L) force fields were 
developed almost completely with TIP4P water. "
Also, David van der spoel had a paper with  Erik Lindahl (JPCB 2003, 
117, 11178-11187) confirming: "OPLS works better with TIP4P".


However, many simulations using OPLS with SPC or TIP3P.

Alan Wilter S. da Silva said in 
http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.html that


"I did short tests with spce and I got a paper with Dr. der Spoel." 
But I can not find any paper for OPLS-AA and SPC/E water.


Suggestions or references are welcomed.


Well, there's this one that endorses SPC/E for several properties:

http://dx.doi.org/10.1021/jp0641029

What you've asked is extremely broad.  Different force fields and solvent models 
can be combined in a number of ways to measure various quantities.  It all comes 
down to what you're hoping to measure.  Is it protein conformational sampling? 
Reproducing NMR signals?  Hydration energies or other thermodynamic properties? 
 Then there's the complication of whether or not OPLS-AA is inherently the best 
choice to represent your protein for these endeavors.  There has been a wealth 
of recent literature on force field comparisons for protein dynamics, as well.


-Justin


Thanks.

Jianhui








--


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] compression- NPT

[Mark Abraham]

On 14/04/2011 4:36 AM, Moeed wrote:

Hello everyone,

I have encountered a strange behavior while compressing a pure system.

I am applying 100 bar pressure with PME and it turned out that this 
pressure leads to density of 20 SI. Changing PME to SHIFT compresses 
the system to density of above 600 SI!! and I should add that PME and 
shift on my system give essentially identical results ( I mean all 
those properties listed in g_energy)


Why are you changing units of pressure mid-sentence?

Also, when I take a configuration from a run which is compressed to a 
higher density which is still off the desired density, applying a even 
higher pressure in the next run not only does not leads to further 
compression but causes the box expand to a much bigger size!


All this sounds so wildly unlikely that you must be mismatching files, 
or similar. Start from a fresh working directory and see what you can 
reproduce. Extraordinary claims require extraordinary evidence.


Mark
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[gmx-users] NPT issue in 4.0.7 and 4.5.3

[Moeed]

Hello,

I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is
giving density of above 600SI (4.0.7) and the other density of around 15 SI
(4.5.3). With 4.5.3 applying 100 bar pressure does not comrades the system
either to the desired density. I need to study the system at different
pressures from 1 to 70 bar, and I am wondering if the system can not be
compressed with these ref_p values how can I keep the pressure fixed at P <
70 bar!?

Please help if you have any idea on why these two versions are giving
inconsistent results and which one is reliable.

Thanks so much,


4.0.7

Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps ],* 14 data sets
The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Angle   36.9945   0.806738   0.804483  0.0521993
0.208798
Ryckaert-Bell.  9.04227   0.376253   0.371412  0.0521057
0.208424
LJ-14   5.23048   0.119612   0.119611 0.00033983
0.00135933
Coulomb-14 -1.66329   0.104171   0.102175  0.0175753
0.0703015
LJ (SR)-27.3967  0  0  0.0421934
0.168774
Coulomb (SR)8.98711   0.1635790.16062 -0.0268199
-0.10728
Potential   31.1944  0  0   0.137594
0.550377
Kinetic En. 51.1009   0.987759   0.987724 0.00725949
0.0290381
Total Energy82.2953  0  0   0.144851
0.579408
Temperature  299.985.798495.79828 0.000340897
0.170449
*Pressure (bar)  69.3587414.279414.256  0.0298385
14.9193*
Cons. rmsd ()4.01744e-06 1.41883e-07 1.41883e-07
0  0
*Box-X   3.04882  0  0 3.57512e-06
0.00178757
Box-Y   3.04882  0  0 3.57512e-*


-
4.5.3.

[* 1500.0001 thru 2000.0001 ps ],*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Angle   37.1357  0.071   0.812307  -0.099711
(kJ/mol)
Ryckaert-Bell.  9.17677   0.14   0.445934  -0.529281
(kJ/mol)
LJ-14   5.18878 0.0087   0.137673   -0.03119
(kJ/mol)
Coulomb-14 -1.60372  0.051   0.126405  -0.144403
(kJ/mol)
LJ (SR)-4.24478   0.29   0.742141   0.697187
(kJ/mol)
Coulomb (SR)8.97451  0.082   0.198278   0.232025
(kJ/mol)
Potential   54.6272   0.311.20733   0.124627
(kJ/mol)
Kinetic En. 51.1047  0.021 0.9945  -0.066306
(kJ/mol)
Total Energy105.732   0.311.58869   0.058321
(kJ/mol)
Temperature 300.002   0.125.83806  -0.389239  (K)
*Pressure 66.7345.3  91.8311.5294  (bar)
*
Constr. rmsd 2.2661e-102.3e-10 3.58302e-08 -1.3595e-09  ()
*Box-X   11.0055  0.082   0.175309  -0.496198  (nm)
Box-Y   11.0055  0.082   0.175309  -0.496198  (nm)*






pbc  =  xyz

integrator  =  md
dt  =  0.002
nsteps  =  100
nstcomm =  100
nstenergy   =  100
nstxout =  100

nstlist =  10
ns_type =  grid

coulombtype =  Shift
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.0

Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300


Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  1
compressibility =  4.5e-5 4.5e-5
ref_p   =  70


gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


constraints = all-bonds
constraint-algorithm = lincs
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[gmx-users] Re: NPT issue in 4.0.7 and 4.5.3

[xiaowu759]

Dear Moeed,
   You seem to be encountering same problem to mine, which was posted to this 
list, .titled "Unexpected results arising from T- and P-coupling methods". Some 
gmxers responded it. You can look for and see them. I wish they can be helpful 
to deal with your problem.
  
 Chaofu Wu, Dr.
  --
 
Date: Wed, 13 Apr 2011 20:22:02 -0400
From: Moeed 
Subject: [gmx-users] NPT issue in 4.0.7 and 4.5.3
To: gmx-users@gromacs.org
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is
giving density of above 600SI (4.0.7) and the other density of around 15 SI
(4.5.3). With 4.5.3 applying 100 bar pressure does not comrades the system
either to the desired density. I need to study the system at different
pressures from 1 to 70 bar, and I am wondering if the system can not be
compressed with these ref_p values how can I keep the pressure fixed at P <
70 bar!?

Please help if you have any idea on why these two versions are giving
inconsistent results and which one is reliable.

Thanks so much,


4.0.7

Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps ],* 14 data sets
The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Angle   36.9945   0.806738   0.804483  0.0521993
0.208798
Ryckaert-Bell.  9.04227   0.376253   0.371412  0.0521057
0.208424
LJ-14   5.23048   0.119612   0.119611 0.00033983
0.00135933
Coulomb-14 -1.66329   0.104171   0.102175  0.0175753
0.0703015
LJ (SR)-27.3967  0  0  0.0421934
0.168774
Coulomb (SR)8.98711   0.1635790.16062 -0.0268199
-0.10728
Potential   31.1944  0  0   0.137594
0.550377
Kinetic En. 51.1009   0.987759   0.987724 0.00725949
0.0290381
Total Energy82.2953  0  0   0.144851
0.579408
Temperature  299.985.798495.79828 0.000340897
0.170449
*Pressure (bar)  69.3587414.279414.256  0.0298385
14.9193*
Cons. rmsd ()4.01744e-06 1.41883e-07 1.41883e-07
0  0
*Box-X   3.04882  0  0 3.57512e-06
0.00178757
Box-Y   3.04882  0  0 3.57512e-*


-
4.5.3.

[* 1500.0001 thru 2000.0001 ps ],*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Angle   37.1357  0.071   0.812307  -0.099711
(kJ/mol)
Ryckaert-Bell.  9.17677   0.14   0.445934  -0.529281
(kJ/mol)
LJ-14   5.18878 0.0087   0.137673   -0.03119
(kJ/mol)
Coulomb-14 -1.60372  0.051   0.126405  -0.144403
(kJ/mol)
LJ (SR)-4.24478   0.29   0.742141   0.697187
(kJ/mol)
Coulomb (SR)8.97451  0.082   0.198278   0.232025
(kJ/mol)
Potential   54.6272   0.311.20733   0.124627
(kJ/mol)
Kinetic En. 51.1047  0.021 0.9945  -0.066306
(kJ/mol)
Total Energy105.732   0.311.58869   0.058321
(kJ/mol)
Temperature 300.002   0.125.83806  -0.389239  (K)
*Pressure 66.7345.3  91.8311.5294  (bar)
*
Constr. rmsd 2.2661e-102.3e-10 3.58302e-08 -1.3595e-09  ()
*Box-X   11.0055  0.082   0.175309  -0.496198  (nm)
Box-Y   11.0055  0.082   0.175309  -0.496198  (nm)*






pbc  =  xyz

integrator  =  md
dt  =  0.002
nsteps  =  100
nstcomm =  100
nstenergy   =  100
nstxout =  100

nstlist =  10
ns_type =  grid

coulombtype =  Shift
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.0

Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300


Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  1
compressibility =  4.5e-5 4.5e-5
ref_p   =  70


gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


constraints = all-bonds
constraint-algorithm = lincs-- 
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[gmx-users] saving coordinates

[Nilesh Dhumal]

Hello,


If some part of molecule is outside the box. How Gromacs save the
coordinates in trajectory.


Nilesh



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Re: [gmx-users] saving coordinates

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,


If some part of molecule is outside the box. How Gromacs save the
coordinates in trajectory.



There is no such thing as "outside" in a periodic system.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin



Nilesh





--


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] NPT issue in 4.0.7 and 4.5.3

[Mark Abraham]

On 14/04/2011 10:22 AM, Moeed wrote:

Hello,

I have run 2 ns simulations on a hydrocarbon system (initial density 
of ~ 2 SI and box size is 15 nm), one with version 4.0.7 and the other 
trial using 4.5.3. Both runs are almost equilibrated to 70 bar 
pressure but one is giving density of above 600SI (4.0.7) and the 
other density of around 15 SI (4.5.3). With 4.5.3 applying 100 bar 
pressure does not comrades the system either to the desired density. I 
need to study the system at different pressures from 1 to 70 bar, and 
I am wondering if the system can not be compressed with these ref_p 
values how can I keep the pressure fixed at P < 70 bar!?


Please help if you have any idea on why these two versions are giving 
inconsistent results and which one is reliable.


Why are your potential energies positive? What does the final 
configuration look like? Why aren't you doing a "simulated annealing" 
style of compression with small increments of delta-P? (These, 
coincidentally are even good data for your study...) Massive leaps in 
ensemble conditions are often poorly-conditioned for numerical 
integration. You're generating velocities that are only approximately 
correct, not giving them any chance to equilibrate, and then smashing 
the system with massive over-pressure. Small wonder it might sometimes 
break...


When reporting output from .log file and g_energy, please either use 
plain text email, or switch to a non-proportional font like Courier. 
Those tables make it harder for people to help you than you want it to be.


Mark



4.0.7

Statistics over 250001 steps [*1500.0001 thru 2000.0001 ps ],* 14 data 
sets

The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps

Energy  Average   RMSD Fluct.  Drift  
Tot-Drift

---
Angle   36.9945   0.806738   0.804483  0.0521993   
0.208798
Ryckaert-Bell.  9.04227   0.376253   0.371412  0.0521057   
0.208424
LJ-14   5.23048   0.119612   0.119611 0.00033983 
0.00135933
Coulomb-14 -1.66329   0.104171   0.102175  0.0175753  
0.0703015
LJ (SR)-27.3967  0  0  0.0421934   
0.168774
Coulomb (SR)8.98711   0.1635790.16062 -0.0268199   
-0.10728
Potential   31.1944  0  0   0.137594   
0.550377
Kinetic En. 51.1009   0.987759   0.987724 0.00725949  
0.0290381
Total Energy82.2953  0  0   0.144851   
0.579408
Temperature  299.985.798495.79828 
0.000340897   0.170449
*Pressure (bar)  69.3587414.279414.256  
0.029838514.9193*
Cons. rmsd ()4.01744e-06 1.41883e-07 1.41883e-07  
0  0
*Box-X   3.04882  0  0 3.57512e-06 
0.00178757

Box-Y   3.04882  0  0 3.57512e-*


-
4.5.3.

[*1500.0001 thru 2000.0001 ps ],*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Angle   37.1357  0.071   0.812307  -0.099711  
(kJ/mol)
Ryckaert-Bell.  9.17677   0.14   0.445934  -0.529281  
(kJ/mol)
LJ-14   5.18878 0.0087   0.137673   -0.03119  
(kJ/mol)
Coulomb-14 -1.60372  0.051   0.126405  -0.144403  
(kJ/mol)
LJ (SR)-4.24478   0.29   0.742141   0.697187  
(kJ/mol)
Coulomb (SR)8.97451  0.082   0.198278   0.232025  
(kJ/mol)
Potential   54.6272   0.311.20733   0.124627  
(kJ/mol)
Kinetic En. 51.1047  0.021 0.9945  -0.066306  
(kJ/mol)
Total Energy105.732   0.311.58869   0.058321  
(kJ/mol)

Temperature 300.002   0.125.83806  -0.389239  (K)
*Pressure 66.7345.3  91.8311.5294  
(bar)*

Constr. rmsd 2.2661e-102.3e-10 3.58302e-08 -1.3595e-09  ()
*Box-X   11.0055  0.082   0.175309  -0.496198  
(nm)
Box-Y   11.0055  0.082   0.175309  -0.496198  
(nm)*







pbc  =  xyz

integrator  =  md
dt  =  0.002
nsteps  =  100
nstcomm =  100
nstenergy   =  100
nstxout =  100

nstlist =  10
ns_type =  grid

coulombtype =  Shift
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.0

Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300


Pcoupl  =  berendsen
Pcoupltype  =  isotro

Re: [gmx-users] compression- NPT

[Moeed]

On 13 April 2011 17:14, Mark Abraham  wrote:

> On 14/04/2011 4:36 AM, Moeed wrote:
>
>> Hello everyone,
>>
>> I have encountered a strange behavior while compressing a pure system.
>>
>> I am applying 100 bar pressure with PME and it turned out that this
>> pressure leads to density of 20 SI. Changing PME to SHIFT compresses the
>> system to density of above 600 SI!! and I should add that PME and shift on
>> my system give essentially identical results ( I mean all those properties
>> listed in g_energy)
>>
>
> Why are you changing units of pressure mid-sentence?


Thanks Mark. I am trying two different runs using shift and PME and use the
same input files..just to see the difference between these two coulomb
types..

>
>
>  Also, when I take a configuration from a run which is compressed to a
>> higher density which is still off the desired density, applying a even
>> higher pressure in the next run not only does not leads to further
>> compression but causes the box expand to a much bigger size!
>>
>
> All this sounds so wildly unlikely that you must be mismatching files, or
> similar. Start from a fresh working directory and see what you can
> reproduce. Extraordinary claims require extraordinary evidence.
>
> Mark
> --
> 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/Search before 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
>
-- 
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Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

[Moeed]

On 13 April 2011 18:45, Mark Abraham  wrote:

>  On 14/04/2011 10:22 AM, Moeed wrote:
>
> Hello,
>
> I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
> SI and box size is 15 nm), one with version 4.0.7 and the other trial using
> 4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is
> giving density of above 600SI (4.0.7) and the other density of around 15 SI
> (4.5.3). With 4.5.3 applying 100 bar pressure does not comrades the system
> either to the desired density. I need to study the system at different
> pressures from 1 to 70 bar, and I am wondering if the system can not be
> compressed with these ref_p values how can I keep the pressure fixed at P <
> 70 bar!?
>
> Please help if you have any idea on why these two versions are giving
> inconsistent results and which one is reliable.
>
>
> Why are your potential energies positive? What does the final configuration
> look like? Why aren't you doing a "simulated annealing" style of compression
> with small increments of delta-P? (These, coincidentally are even good data
> for your study...) Massive leaps in ensemble conditions are often
> poorly-conditioned for numerical integration. You're generating velocities
> that are only approximately correct, not giving them any chance to
> equilibrate, and then smashing the system with massive over-pressure. Small
> wonder it might sometimes break...
>

Hi Mark,

You mean I should get negative potential? I am sure topology is generated
properly. can you explain why this is concerning?


Can you please elaborate on compressing using simulated annealing? How can I
do this?

Thanks, :)



>
> When reporting output from .log file and g_energy, please either use plain
> text email, or switch to a non-proportional font like Courier. Those tables
> make it harder for people to help you than you want it to be.
>
> Mark
>
>
>
> 4.0.7
>
> Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps ],* 14 data
> sets
> The term 'Cons. rmsd ()' is averaged over 2501 frames
> All other averages are exact over 250001 steps
>
> Energy  Average   RMSD Fluct.  Drift
> Tot-Drift
>
> ---
> Angle   36.9945   0.806738   0.804483  0.0521993
> 0.208798
> Ryckaert-Bell.  9.04227   0.376253   0.371412  0.0521057
> 0.208424
> LJ-14   5.23048   0.119612   0.119611 0.00033983
> 0.00135933
> Coulomb-14 -1.66329   0.104171   0.102175  0.0175753
> 0.0703015
> LJ (SR)-27.3967  0  0  0.0421934
> 0.168774
> Coulomb (SR)8.98711   0.1635790.16062 -0.0268199
> -0.10728
> Potential   31.1944  0  0   0.137594
> 0.550377
> Kinetic En. 51.1009   0.987759   0.987724 0.00725949
> 0.0290381
> Total Energy82.2953  0  0   0.144851
> 0.579408
> Temperature  299.985.798495.79828 0.000340897
> 0.170449
> *Pressure (bar)  69.3587414.279414.256  0.0298385
> 14.9193*
> Cons. rmsd ()4.01744e-06 1.41883e-07 1.41883e-07
> 0  0
> *Box-X   3.04882  0  0 3.57512e-06
> 0.00178757
> Box-Y   3.04882  0  0 3.57512e-*
>
>
> -
> 4.5.3.
>
> [* 1500.0001 thru 2000.0001 ps ],*
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Angle   37.1357  0.071   0.812307  -0.099711
> (kJ/mol)
> Ryckaert-Bell.  9.17677   0.14   0.445934  -0.529281
> (kJ/mol)
> LJ-14   5.18878 0.0087   0.137673   -0.03119
> (kJ/mol)
> Coulomb-14 -1.60372  0.051   0.126405  -0.144403
> (kJ/mol)
> LJ (SR)-4.24478   0.29   0.742141   0.697187
> (kJ/mol)
> Coulomb (SR)8.97451  0.082   0.198278   0.232025
> (kJ/mol)
> Potential   54.6272   0.311.20733   0.124627
> (kJ/mol)
> Kinetic En. 51.1047  0.021 0.9945  -0.066306
> (kJ/mol)
> Total Energy105.732   0.311.58869   0.058321
> (kJ/mol)
> Temperature 300.002   0.125.83806  -0.389239  (K)
> *Pressure 66.7345.3  91.8311.5294
> (bar)*
> Constr. rmsd 2.2661e-102.3e-10 3.58302e-08 -1.3595e-09  ()
> *Box-X   11.0055  0.082   0.175309  -0.496198
> (nm)
> Box-Y   11.0055  0.082   0.175309  -0.496198  (nm)
> *
>
>
>
>
>
>
> pbc  =  xyz
>
> integrator  =  md
> dt  =  0.002
> nsteps  =  100
> nstcomm =  100
> nstenergy   =  100
> nstxout =  100
>
> nstlist 

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

[Mark Abraham]

On 14/04/2011 3:40 PM, Moeed wrote:



On 13 April 2011 18:45, Mark Abraham > wrote:


On 14/04/2011 10:22 AM, Moeed wrote:

Hello,

I have run 2 ns simulations on a hydrocarbon system (initial
density of ~ 2 SI and box size is 15 nm), one with version 4.0.7
and the other trial using 4.5.3. Both runs are almost
equilibrated to 70 bar pressure but one is giving density of
above 600SI (4.0.7) and the other density of around 15 SI
(4.5.3). With 4.5.3 applying 100 bar pressure does not comrades
the system either to the desired density. I need to study the
system at different pressures from 1 to 70 bar, and I am
wondering if the system can not be compressed with these ref_p
values how can I keep the pressure fixed at P < 70 bar!?

Please help if you have any idea on why these two versions are
giving inconsistent results and which one is reliable.


Why are your potential energies positive? What does the final
configuration look like? Why aren't you doing a "simulated
annealing" style of compression with small increments of delta-P?
(These, coincidentally are even good data for your study...)
Massive leaps in ensemble conditions are often poorly-conditioned
for numerical integration. You're generating velocities that are
only approximately correct, not giving them any chance to
equilibrate, and then smashing the system with massive
over-pressure. Small wonder it might sometimes break...


Hi Mark,

You mean I should get negative potential? I am sure topology is 
generated properly. can you explain why this is concerning?


What does a set of charges with positive potential energy want to do?

Can you please elaborate on compressing using simulated annealing? How 
can I do this?


That's not what I said - I used quotation marks and the word "style" for 
a reason. I told you not to do massive changes of conditions, and to use 
small increments of delta-P. Equilibrate at one P, change it a bit. 
Repeat. This is like simulated annealing, but with P instead of T.


Mark


Thanks, :)


When reporting output from .log file and g_energy, please either
use plain text email, or switch to a non-proportional font like
Courier. Those tables make it harder for people to help you than
you want it to be.

Mark




4.0.7

Statistics over 250001 steps [*1500.0001 thru 2000.0001 ps ],* 14
data sets
The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps

Energy  Average   RMSD Fluct. 
Drift  Tot-Drift


---
Angle   36.9945   0.806738   0.804483 
0.0521993   0.208798
Ryckaert-Bell.  9.04227   0.376253   0.371412 
0.0521057   0.208424

LJ-14   5.23048   0.119612   0.119611
0.00033983 0.00135933
Coulomb-14 -1.66329   0.104171   0.102175 
0.0175753  0.0703015
LJ (SR)-27.3967  0  0 
0.0421934   0.168774

Coulomb (SR)8.98711   0.1635790.16062
-0.0268199   -0.10728
Potential   31.1944  0  0  
0.137594   0.550377

Kinetic En. 51.1009   0.987759   0.987724
0.00725949  0.0290381
Total Energy82.2953  0  0  
0.144851   0.579408

Temperature  299.985.798495.79828
0.000340897   0.170449
*Pressure (bar)  69.3587414.279414.256 
0.029838514.9193*

Cons. rmsd ()4.01744e-06 1.41883e-07
1.41883e-07  0  0
*Box-X   3.04882  0  0
3.57512e-06 0.00178757
Box-Y   3.04882  0  0 3.57512e-*


-
4.5.3.

[*1500.0001 thru 2000.0001 ps ],*

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Angle   37.1357  0.071   0.812307 
-0.099711  (kJ/mol)
Ryckaert-Bell.  9.17677   0.14   0.445934 
-0.529281  (kJ/mol)
LJ-14   5.18878 0.0087   0.137673  
-0.03119  (kJ/mol)
Coulomb-14 -1.60372  0.051   0.126405 
-0.144403  (kJ/mol)
LJ (SR)-4.24478   0.29   0.742141  
0.697187  (kJ/mol)
Coulomb (SR)8.97451  0.082   0.198278  
0.232025  (kJ/mol)
Potential   54.6272   0.311.20733  
0.124627  (kJ/mol)
Kinetic En. 51.1047  0.021 0.9945 
-0.066306  (kJ/mol)
Total Energy105.732   0.311.58869  
0.05

Re: [gmx-users] compression- NPT

[Mark Abraham]

On 14/04/2011 2:53 PM, Moeed wrote:



On 13 April 2011 17:14, Mark Abraham > wrote:


On 14/04/2011 4:36 AM, Moeed wrote:

Hello everyone,

I have encountered a strange behavior while compressing a pure
system.

I am applying 100 bar pressure with PME and it turned out that
this pressure leads to density of 20 SI. Changing PME to SHIFT
compresses the system to density of above 600 SI!! and I
should add that PME and shift on my system give essentially
identical results ( I mean all those properties listed in
g_energy)


Why are you changing units of pressure mid-sentence?


Thanks Mark. I am trying two different runs using shift and PME and 
use the same input files..just to see the difference between these two 
coulomb types..


For a hydrocarbon system, which is not strongly charged, it won't matter 
much.


Mark




Also, when I take a configuration from a run which is
compressed to a higher density which is still off the desired
density, applying a even higher pressure in the next run not
only does not leads to further compression but causes the box
expand to a much bigger size!


All this sounds so wildly unlikely that you must be mismatching
files, or similar. Start from a fresh working directory and see
what you can reproduce. Extraordinary claims require extraordinary
evidence.

Mark
-- 
gmx-users mailing list gmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before 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




-- 
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/Search before 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