[gmx-users] Wrong pressure with "mdrun -rerun" option

[LuLanyuan]

Hello all,
>From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be 
>correct. However, I did a test for a box of tip3p water and found the pressure 
>results from rerun were different compared to the original results. For the 
>first MD simulation , I simulated it for 200 ps and use the neighbor list 
>update frequency 1. I used "g_energy" to extract pressure results and the 
>results were 545.384 and 1153.55 bars for the MD and rerun, respectively. The 
>gromacs version is 4.0.5.
Can anyone give me any clue?
Thanks.
Lanyuan Lu

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[gmx-users] A question regarding single sum virial

[LuLanyuan]

Hello all,
I got a question when I read the the manual chapter for the single sum virial 
(p195-196).  In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't  delta here 
also depend on index j? I think delta is zero when particle i and j are close. 
And delta can be something else when any x/y/z component of r_i-r_j is larger 
than half box length. But from eq (B.5) to (B.11) it seems delta_i only depends 
on index i and I got confused.
Could anyone explain it to me?
Thanks very much!
Lanyuan Lu

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RE: [gmx-users] A question regarding single sum virial

[LuLanyuan]

That's cool. Thanks a lot!
Lanyuan

> Date: Wed, 12 Aug 2009 22:01:14 +0200
> Subject: Re: [gmx-users] A question regarding single sum virial
> From: tsje...@gmail.com
> To: gmx-users@gromacs.org
> 
> Hi Lanyuan Lu,
> 
> It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available 
> at:
> http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/
> 
> Cheers,
> 
> Tsjerk
> 
> 2009/8/12 LuLanyuan :
> > Hello all,
> > I got a question when I read the the manual chapter for the single sum
> > virial (p195-196).  In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't
> > delta here also depend on index j? I think delta is zero when particle i and
> > j are close. And delta can be something else when any x/y/z component of
> > r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems
> > delta_i only depends on index i and I got confused.
> > Could anyone explain it to me?
> > Thanks very much!
> > Lanyuan Lu
> >
> > 
> > 使用新一代 Windows Live Messenger 轻松交流和共享！ 立刻下载！
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> >
> 
> 
> 
> -- 
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> 3584 CH Utrecht
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RE: [gmx-users] A question regarding single sum virial

[LuLanyuan]

Hello,
Unfortunately I still don't understand the equations in the manual after 
reading Chapter 2 of Hendrik Bekker's dissertation. In that chapter, the virial 
is expressed as A+B+C. 
Here A+B is the r_i*F_i stuff, which can be considered as the virial without 
considering PBC. And the third term should correspond to the detla derm in the 
Gromacs manual, which is a correction due to PBC. However, in the dissertation 
the correction term is always related to pairwise forces F_ij in different ways 
to calculate it. In the manual, the correction term is written as delta_i*F_i, 
which is related to individual force on each atom only. I still have no idea 
for that how the magic delta can convert a pairwise force expression into an 
individual force expression.
Anyone has an idea about it?
Thanks,
Lanyuan

> Date: Wed, 12 Aug 2009 22:01:14 +0200
> Subject: Re: [gmx-users] A question regarding single sum virial
> From: tsje...@gmail.com
> To: gmx-users@gromacs.org
> 
> Hi Lanyuan Lu,
> 
> It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available 
> at:
> http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/
> 
> Cheers,
> 
> Tsjerk
> 
> 2009/8/12 LuLanyuan :
> > Hello all,
> > I got a question when I read the the manual chapter for the single sum
> > virial (p195-196).  In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't
> > delta here also depend on index j? I think delta is zero when particle i and
> > j are close. And delta can be something else when any x/y/z component of
> > r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems
> > delta_i only depends on index i and I got confused.
> > Could anyone explain it to me?
> > Thanks very much!
> > Lanyuan Lu
> >
> > 
> > 使用新一代 Windows Live Messenger 轻松交流和共享！ 立刻下载！
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> ___
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RE: [gmx-users] user defined potential function for 1-4 interaction

[LuLanyuan]

Hi,
As I remember, you can only use one table for 1-4 interactions. Don't know if 
it's changed
in the latest version.
Lanyuan

> From: mhrah...@dal.ca
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] user defined potential function for 1-4 interaction
> Date: Thu, 8 Oct 2009 19:10:39 -0300
> 
> Hi all:
> I posted this earlier but did not get  any help I really need to slove this 
> issue.
> 
> What should be the way to pass a formatted table for the 1-4 interaction
>  for two or more different groups? Reading  page 150  and 180 of manual 4.0, 
> I
>  understand user defined potential functions can be passed for many groups
>  using  energygrp_table in .mdp file but nothing is clearly mentioned
>  regarding pair interaction
> 
> I have two grps for 1-4 interactions MTN and SFT.
> mdrun command includes:
> -table table.xvg   -tablep pair.xvg
> .mdp file contains,
> energygrps = MTN SFT
> energygrp_table: MTN MTN MTN SFT
> 
> I  passed three tables for pair interaction in the
>  name pair.xvg,  pair_MTN_MTN.xvg and  pair_MTN_SFT.xvg.
> I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and 
> pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning.
> I am afraid that I failed to submit  separate table for pair interaction 
> properly in this way.
> 
> Thanks,
> M.H.Rahman 
> 
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[gmx-users] interpolation for tabulated potential

[LuLanyuan]

Hello,
I'm just wondering what interpolation method is used for the tabulated 
potential function in GMX. Since GMX 4, the input table contains potential and 
force, unlike potential and second derivative in GMX 3. Is cubic spline still 
used in GMX 4? If yes, what algorithm is implemented to get second derivative 
needed for cubic spline?
Thanks,
Lanyuan
  
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RE: [gmx-users] interpolation for tabulated potential

[LuLanyuan]

I saw it. Thanks.
Lanyuan

> Date: Wed, 14 Oct 2009 14:50:02 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] interpolation for tabulated potential
> 
> LuLanyuan wrote:
> > Hello,
> > I'm just wondering what interpolation method is used for the tabulated 
> > potential function in GMX. Since GMX 4, the input table contains 
> > potential and force, unlike potential and second derivative in GMX 3. Is 
> > cubic spline still used in GMX 4? If yes, what algorithm is implemented 
> > to get second derivative needed for cubic spline?
> 
> That's all in the manual. Please start there.
> 
> Mark
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[gmx-users] weird tabulated potential problem

[LuLanyuan]

Hi,
Some months ago I reported a strange conflict between the GMX 4 new option 
nblist=-1 and tabulated potentials. At that time I contacted Berk and he could 
run my test system without any problem. So I thought I had something wrong for 
my system configurations. However, recently I re-checked the problem and found 
I got similar issues from two different software/hardware configurations. It 
seems the problem is sort of general. I'm wondering if any developer or people 
who are familiar with the code can help me to figure out the problem.
The problem is like the follows. When I use nblist=-1 option with tabulated 
nonbond interation, sometimes I got a segmatation fault. I used nonebond tables 
with space 0.004 nm and I smoothed the curves so no complain of wrong numerical 
derivatives from GMX were found. I tested the simulation on three machines:
A: Intel i7 gcc 4.1.2
B: Intel Xeon icc 10.1
C: AMD Barcelona icc 10.1
All tests were done using one CPU core. It seems system A/B always gave me 
troubles and C was fine.
I first used rlist =1.3 and rvdw=1.2 to give a 0.1 buffer. And I found the 
potential energys from A/B were weired with values sometimes as 1.0e29. And the 
potential energy with C is always around 1.0e3. When I set rlist=1.28, I can 
optimize the "Average neighborlist lifetime" about 11, as Berk onece suggested. 
But in this buffer size, simulations with A/B got segmentation fault 
immediately. Interestingly, I tried to try many conventional force field 
simulations/CG simulations with tabulated potentials before with A/B, and all 
of them seemed to be fine if I didn't use nblist=-1 with tabulated potentials.
Can anyone give me any suggestions?
Thanks,
Lanyuan
  
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RE: [gmx-users] question about all atoms lipid molecule structure and force field

[LuLanyuan]

Hi,
You can find some configurations here:
http://persweb.wabash.edu/facstaff/fellers/
And I think you can use Charmm FF.
Lanyuan

Date: Wed, 14 Oct 2009 11:29:26 -0700
From: kgp.a...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] question about all atoms lipid molecule structure and  
force field

Dear all,
I have been trying to search for an all atom DPPC sructure (including the 
missing Hydrogens of long chain hydrocarbons) and then do an all atoms md 
simulation on it. I havent yet found any such structure or any force field that 
could be used for it on the internet. Is anybody familiar with any such work ?

Is there any all atom model for hydrocarbons which is incorporated in Gromacs? 
I am not 100 % sure about it.
I want to do this to parametrize another force field which essentially uses all 
atom model.

Thank you,Amit
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[gmx-users] a question about template.c

[LuLanyuan]

Hello,
When I used template.c to make my own tool,  I always got the progress 
information like
"Reading frame  60 time   60.000" after the Gromacs copyright information. 
Sometimes
I want to run my tool in background. But these reading frame messages still 
jump out even 
after I use the "&" command. Because I may need to do other things in the same 
terminal,
these messages are annoying. I'm wondering if there is a simple way to redirect 
these outputs.
Thanks very much.
Lanyuan Lu 
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RE: [gmx-users] a question about template.c

[LuLanyuan]

Sorry, I didn't say it clearly.
I used command> command.out & and it didn't work. I just tried nohup thing and
it's the same. It seems to me the redirect ">" doesn't work for the reading 
frame 
messages.
Lanyuan

> Date: Mon, 6 Oct 2008 17:22:44 -0600
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] a question about template.c
> 
> LuLanyuan a écrit :
>> Hello,
>> When I used template.c to make my own tool,  I always got the progress 
>> information like
>> "Reading frame  60 time   60.000" after the Gromacs copyright 
>> information. Sometimes
>> I want to run my tool in background. But these reading frame messages still 
>> jump out even 
>> after I use the "&" command. Because I may need to do other things in the 
>> same terminal,
>> these messages are annoying. I'm wondering if there is a simple way to 
>> redirect these outputs.
>> Thanks very much.
>> Lanyuan Lu 
>>   
> command>& command.out
> or
> nohup command &
> 
> depending what you want to do
> 
> cheers
>> _
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>> http://im.live.cn/emoticons/?ID=18
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>>
>>   
> 

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RE: [gmx-users] a question about template.c

[LuLanyuan]

Hello,
I think it works as "command>& command.out &". That's just what I need.
Thank you all very much.
Lanyuan

> Date: Tue, 7 Oct 2008 01:36:58 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] a question about template.c
> 
> * Nicolas  [2008-10-06 17:22:44 -0600]:
> 
>>LuLanyuan a écrit :
>>> Hello,
>>> When I used template.c to make my own tool,  I always got the progress 
>>> information like
>>> "Reading frame  60 time   60.000" after the Gromacs copyright 
>>> information. Sometimes
>>> I want to run my tool in background. But these reading frame messages still 
>>> jump out even 
>>> after I use the "&" command. Because I may need to do other things in the 
>>> same terminal,
>>> these messages are annoying. I'm wondering if there is a simple way to 
>>> redirect these outputs.
>>> Thanks very much.
>>> Lanyuan Lu 
>>>   
>>command>& command.out
>>or
>>nohup command &
>>
>>depending what you want to do
>>
>>cheers
>   And to provide a small explanation, you see this line, because it is
>   written to the stderr. If you use just '>' only the stdout is written
>   to the file. '>&' bundles both the stderr and stdout to one single
>   file.
> 
>   /Flo
>>> _
>>> ??MSNTA??
>>> http://im.live.cn/emoticons/?ID=18
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>>>
>>>
>>>   
>>
> 
> 
>>___
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> 
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> 
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[gmx-users] "nstlist=-1" and performance problem

[LuLanyuan]

Hello,
Could Berk or someone else answer my question regarding the new "nstlist=-1" 
option in gmx4? In my understanding, the algorithm for this option is the one 
used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with 
"nstlist=-1" and "nstlist=1", I found the speeds were basically the same. Isn't 
this automatic nblist checking supposed to be faster than updating the nblist 
every step? I also did similar tests on LAMMPS for the same system and found 
the speed for automatical updating was several times faster. As a result, 
although Gromacs is about 60% faster if we choose nstlist=1,  it's much slower 
than LAMMPS if we choose the automatic nblist updating. 
Thanks in advance for any ideas about it.
Lanyuan Lu


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RE: [gmx-users] "nstlist=-1" and performance problem

[LuLanyuan]

Hi Berk,
Thanks very much. I've found the problem. As you said I forgot to increase 
rvdw. So the buffer is zero and the system needs to update the nblist every 
step, which is obviously wrong. After I corrected the mistake, the speed for 
"nstlist=-1" is roughly three times faster as I expected.
Lanyuan

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 10:42:59 +0100








Hi,

I assume you did not only change nstlist, but also other mdp settings, or not?

Changing only nstlist from 1 to -1 should result in nearly equal or much faster 
speeds.

For efficient simulations with nslist=-1 you need to set an appropriate
buffer region (rlist > rcoulomb=rvdw). In 4.0 you have to optimize this by hand.
It would be nice to have this automated.
At the end of the log file (a run of a few minutes is enough) you can see what
the neighborlist lifetime is. Optimal is usually something between 10 and 20.
Play with rlist to optimize the performance (also printed at the end of the log 
file).

Berk

From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Mon, 26 Jan 2009 17:31:43 -0500
Subject: [gmx-users] "nstlist=-1" and performance problem








Hello,
Could Berk or someone else answer my question regarding the new "nstlist=-1" 
option in gmx4? In my understanding, the algorithm for this option is the one 
used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with 
"nstlist=-1" and "nstlist=1", I found the speeds were basically the same. Isn't 
this automatic nblist checking supposed to be faster than updating the nblist 
every step? I also did similar tests on LAMMPS for the same system and found 
the speed for automatical updating was several times faster. As a result, 
although Gromacs is about 60% faster if we choose nstlist=1,  it's much slower 
than LAMMPS if we choose the automatic nblist updating. 
Thanks in advance for any ideas about it.
Lanyuan Lu


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RE: [gmx-users] "nstlist=-1" and performance problem

[LuLanyuan]

Hi,
No warning was found. Is it because the use of "User" vdw potential?
The mdp file is the following:

title= A
cpp  = cpp
include  = -I../top
define   =
integrator   = md
dt   = 0.001
nsteps   = 1
nstxout  = 1000
nstvout  = 1000
nstlog   = 1000
nstenergy= 1000
nstxtcout= 0
energygrps   = CGW CBB HAL NBB  OBB
coulombtype  = User
rcoulomb = 1.1
nstlist  = -1
ns_type  = grid
pbc  = xyz
rlist= 1.1
vdwtype  = User
rvdw = 1.1
table-extension  = 0.
energygrp_table  = CGW CGW CGW HAL CGW NBB CGW OBB CGW CBB CBB CBB CBB 
NBB CBB OBB CBB HAL HAL HAL HAL NBB HAL OBB NBB NBB NBB OBB OBB OBB
tcoupl   = nose-hoover
tc_grps  = System
tau_t= 0.1
ref_t= 310
pcoupl   = no
gen_vel  = yes
gen_temp = 310
gen_seed = 173529

Thanks.
Lanyuan

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 23:22:30 +0100








Hi,

But grompp should have given a warning about this.
You should have only obtained a tpr file when using the -maxwarn option of 
grompp.
Or did grompp not give a warning about the buffer being too small?

Berk

From: lulany...@msn.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 17:12:00 -0500








Hi Berk,
Thanks very much. I've found the problem. As you said I forgot to increase 
rvdw. So the buffer is zero and the system needs to update the nblist every 
step, which is obviously wrong. After I corrected the mistake, the speed for 
"nstlist=-1" is roughly three times faster as I expected.
Lanyuan

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 10:42:59 +0100








Hi,

I assume you did not only change nstlist, but also other mdp settings, or not?

Changing only nstlist from 1 to -1 should result in nearly equal or much faster 
speeds.

For efficient simulations with nslist=-1 you need to set an appropriate
buffer region (rlist > rcoulomb=rvdw). In 4.0 you have to optimize this by hand.
It would be nice to have this automated.
At the end of the log file (a run of a few minutes is enough) you can see what
the neighborlist lifetime is. Optimal is usually something between 10 and 20.
Play with rlist to optimize the performance (also printed at the end of the log 
file).

Berk

From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Mon, 26 Jan 2009 17:31:43 -0500
Subject: [gmx-users] "nstlist=-1" and performance problem








Hello,
Could Berk or someone else answer my question regarding the new "nstlist=-1" 
option in gmx4? In my understanding, the algorithm for this option is the one 
used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with 
"nstlist=-1" and "nstlist=1", I found the speeds were basically the same. Isn't 
this automatic nblist checking supposed to be faster than updating the nblist 
every step? I also did similar tests on LAMMPS for the same system and found 
the speed for automatical updating was several times faster. As a result, 
although Gromacs is about 60% faster if we choose nstlist=1,  it's much slower 
than LAMMPS if we choose the automatic nblist updating. 
Thanks in advance for any ideas about it.
Lanyuan Lu


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RE: [gmx-users] "nstlist=-1" and performance problem

[LuLanyuan]

Hi,
It's in the gmx4.0 manual. Just check the part for mdp options. I guess it is 
the method in DLPOLY and many text books.
Lanyuan

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 23:28:25 +0100

Hi,
Any documentation on how this is actually done? 
Sounds interesting!
XAvier.
On Jan 28, 2009, at 11:12 PM, LuLanyuan wrote:Hi Berk,
Thanks very much. I've found the problem. As you said I forgot to increase 
rvdw. So the buffer is zero and the system needs to update the nblist every 
step, which is obviously wrong. After I corrected the mistake, the speed for 
"nstlist=-1" is roughly three times faster as I expected.
Lanyuan

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 10:42:59 +0100

Hi,

I assume you did not only change nstlist, but also other mdp settings, or not?

Changing only nstlist from 1 to -1 should result in nearly equal or much faster 
speeds.

For efficient simulations with nslist=-1 you need to set an appropriate
buffer region (rlist > rcoulomb=rvdw). In 4.0 you have to optimize this by hand.
It would be nice to have this automated.
At the end of the log file (a run of a few minutes is enough) you can see what
the neighborlist lifetime is. Optimal is usually something between 10 and 20.
Play with rlist to optimize the performance (also printed at the end of the log 
file).

Berk

From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Mon, 26 Jan 2009 17:31:43 -0500
Subject: [gmx-users] "nstlist=-1" and performance problem

Hello,
Could Berk or someone else answer my question regarding the new "nstlist=-1" 
option in gmx4? In my understanding, the algorithm for this option is the one 
used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with 
"nstlist=-1" and "nstlist=1", I found the speeds were basically the same. Isn't 
this automatic nblist checking supposed to be faster than updating the nblist 
every step? I also did similar tests on LAMMPS for the same system and found 
the speed for automatical updating was several times faster. As a result, 
although Gromacs is about 60% faster if we choose nstlist=1,  it's much slower 
than LAMMPS if we choose the automatic nblist updating. 
Thanks in advance for any ideas about it.
Lanyuan Lu


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[gmx-users] "nstlist=-1" dosen't work for parallel runs

[LuLanyuan]

Hi,
Again I have a problem regarding the "nstlist=-1" option and this time it's 
related to parallel runs.
With the help from Berk, I can run my system with nstlist=-1 option and 1 cpu 
without any problem. However, each time when I run it using more than one cpu 
under MPI, the run crashes immediately. The input files are the same for both 
serial and parallel runs. I tried to change to nstlist=1 and this time it run 
OK both serial and parallel. So it seems to me there is a problem for the 
automatic neighbor list updating with parallel runs. I tried both domain 
decomposition and particle decompostion with "nstlis=-1" and in both cases the 
run crashed.
Could Berk or anyone else have a look at it?
Thanks very much.
Lanyuan

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RE: [gmx-users] "nstlist=-1" dosen't work for parallel runs

[LuLanyuan]

He Berk,
I've sent it to the bugzilla. Could you have a look?
Thanks very much!
Lanyuan

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=-1" dosen't work for parallel runs
Date: Thu, 29 Jan 2009 23:32:43 +0100








Hi,

I just tested it and it runs fine for me with 4.0.3.

Which version are you using?

If it is 4.0.3, please file a bugzilla and attach the tpr file.

Berk

From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Thu, 29 Jan 2009 15:07:27 -0500
Subject: [gmx-users] "nstlist=-1" dosen't work for parallel runs








Hi,
Again I have a problem regarding the "nstlist=-1" option and this time it's 
related to parallel runs.
With the help from Berk, I can run my system with nstlist=-1 option and 1 cpu 
without any problem. However, each time when I run it using more than one cpu 
under MPI, the run crashes immediately. The input files are the same for both 
serial and parallel runs. I tried to change to nstlist=1 and this time it run 
OK both serial and parallel. So it seems to me there is a problem for the 
automatic neighbor list updating with parallel runs. I tried both domain 
decomposition and particle decompostion with "nstlis=-1" and in both cases the 
run crashed.
Could Berk or anyone else have a look at it?
Thanks very much.
Lanyuan

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[gmx-users] A question regarding the xdr lib

[LuLanyuan]

Hello,
I just compiled the xdr file lib that was recently released on the Gromacs 
website. 
I'm just wondering what's the meaning of "char *fn" in the xdrfile_???.h as in:

/* This function returns the number of atoms in the xtc file in *natoms */
  extern int read_xtc_natoms(char *fn,int *natoms);

  /* Read one frame of an open xtc file */
  extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
  matrix box,rvec *x,float *prec);

Is the "char *fn" the name of the xdr file?
Can anyone give me a clue? Thanks very much.
Lanyuan Lu


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RE: [gmx-users] A question regarding the xdr lib

[LuLanyuan]

Thanks very much, David.
Lanyuan

> Date: Mon, 6 Apr 2009 22:56:43 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] A question regarding the xdr lib
> 
> LuLanyuan wrote:
> > Hello,
> > I just compiled the xdr file lib that was recently released on the 
> > Gromacs website.
> > I'm just wondering what's the meaning of "char *fn" in the xdrfile_???.h 
> > as in:
> > 
> > /* This function returns the number of atoms in the xtc file in *natoms */
> >   extern int read_xtc_natoms(char *fn,int *natoms);
> > 
> >   /* Read one frame of an open xtc file */
> >   extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
> >   matrix box,rvec *x,float *prec);
> > 
> > Is the "char *fn" the name of the xdr file?
> yes.
> 
> please check the test program, for examples.
> 
> > Can anyone give me a clue? Thanks very much.
> > Lanyuan Lu
> > 
> > 
> > 
> > 微软地图实时路况，为您节省的不仅仅是时间！ 立即查看！ 
> > <http://ditu.live.com/default.aspx?v=2&form=MICHAJ&cp=qcbgzzsz1gzz&style=r&lvl=4&tilt=-90&dir=0&alt=-1000&phx=0&phy=0&phscl=1&trfc=1&encType=1>
> > 
> > 
> > 
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> 
> 
> -- 
> David.
> 
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:46 18 471 4205  fax: 46 18 511 755
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
> 
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[gmx-users] What's the max number of pull groups?

[LuLanyuan]

Hello,
Could anyone tell me what the maximum number of COM pulling groups is in GMX 4?
Thanks very much.
Lanyuan Lu 

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RE: [gmx-users] What's the max number of pull groups?

[LuLanyuan]

Thanks so much, Berk. I have another question regarding the pull code. Can I 
define a pull group that contains more than one molecules? I tried to define 
some lipid molecules as a single pull group and pull them out of a bilayer. But 
I couldn't see the lipids out. If I try one lipid as a pull group, I got what I 
expected.
Lanyuan

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] What's the max number of pull groups?
Date: Fri, 10 Apr 2009 23:04:32 +0200








Hi,

There is no maximum.

Berk

From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Fri, 10 Apr 2009 16:04:18 -0400
Subject: [gmx-users] What's the max number of pull groups?








Hello,
Could anyone tell me what the maximum number of COM pulling groups is in GMX 4?
Thanks very much.
Lanyuan Lu 

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[gmx-users] deshuf.ndx doesn't work for forces?

[LuLanyuan]

Hello All,
I found sth like a bug regarding the deshuffle index file. I did a simulation 
using multiple cpus and -sort -shuffle options. After that I tried to use the 
deshuf.ndx file to recover the original atom order for my trr file by trjconv 
-n deshuf.ndx ... command. But by checking the output trr using the gmxdump, I 
found the oders of x and v were deshuffled while the f oder remained unchanged. 
In another word the values of forces were not consistent with those of 
positions and velocities in the new trr file.
Is this a bug? And is there anyway to get the correct oder for forces also?
Thanks a lot.
Lanyuan Lu
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RE: [gmx-users] deshuf.ndx doesn't work for forces?

[LuLanyuan]

Hi,
I think after the "trjconv -f *.trr -n deshuf.ndx" operation,  the new orders 
of x and v in the trr file are correct. 
Here "correct" means the order is the same as the intitial *.gro file you use 
for grompp command. If the output
of trjconv is gro/pdb, you're right that it's only deshuffled, but not 
desorted. But since there's no force in the gro
file, the bug i mentioned is only in the case when you choose trr as the output 
of your deshuffle operation.
Lanyuan Lu

> Date: Thu, 24 Jan 2008 12:28:47 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] deshuf.ndx doesn't work for forces?
> 
>> Message: 2
>> Date: Wed, 23 Jan 2008 18:56:22 -0500
>> From: LuLanyuan 
>> Subject: [gmx-users] deshuf.ndx doesn't work for forces?
>> To: 
>> Message-ID: 
>> Content-Type: text/plain; charset="gb2312"
>>
>>
>> Hello All,
>> I found sth like a bug regarding the deshuffle index file. I did a   
>> simulation using multiple cpus and -sort -shuffle options. After   
>> that I tried to use the deshuf.ndx file to recover the original atom  
>>  order for my trr file by trjconv -n deshuf.ndx ... command.
> 
> As I understand it, the deshuf.ndx file does not allow you to desort,  
> merely to deshuffle.
> 
>> But by checking the output trr using the gmxdump, I found the oders  
>> of x  and v were deshuffled while the f oder remained unchanged. In   
>> another word the values of forces were not consistent with those of   
>> positions and velocities in the new trr file.
>> Is this a bug?
> 
> So the order of the positions and velocities has changed, but are they  
> correct? I do not believe that gromacs 3.3.1 is capable of desorting,  
> nor is it supported. I have uploaded a tool called g_desort to the  
> users contribution section. It works well and is tested, but it's  
> usage is complicated when you want to load in .trr files via grompp.
> 
>> And is there anyway to get the correct oder for forces also?
> 
> I suggest that you try to reproduce this problem while using -shuffle  
> but not -sort.
> 
>> Thanks a lot.
>> Lanyuan Lu
>> _
> 
> 
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RE: [gmx-users] Re: deshuf.ndx doesn't work for forces?

[LuLanyuan]

I think you need to add -force option.
Like trjconv -f a.trr -force -o b.trr
Lanyuan Lu

> Date: Thu, 24 Jan 2008 17:39:45 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: deshuf.ndx doesn't work for forces?
> 
> My apologies, The commands should have been:
> 
> trjconv -f a.trr -o b.trr
> gmxdump -f a.trr> a.dump
> gmxdump -f b.trr> b.dump
> diff a.dump b.dump> ab.diff
> 
> Chris Neale wrote:
>> OK, I can confirm this for 3.3.1. However, I don't think that the 
>> problem is one of shuffling or sorting but simply that
>> trjconv -f a.trr -o b.trr creates an exact copy of the .trr file 
>> *without* the forces. You can easily verify this by doing this:
>>
>> trjconv -f a.trr -o b.trr
>> gmxdump -f a.trr> a.dumo
>> gmxdump -f b.trr> b.trr
>> diff a.trr b.trr> ab.diff
>>
>> Note that b.trr is of smaller size then b.trr and the ab.diff file 
>> clearly shows that it is the forces that are missing.
>>
>> I actually have never tested that before now so it appears that my 
>> g_desort routine will lead to the loss of force information at each 
>> re-sorting event by nature of passing through trjconv -o .trr.
>>
>> I did take a quick look at the gmx_trjconv code but I am unable to 
>> determine the particular place where the code might be changed.
>> However, I think that I have isolated it to the need to add an output 
>> of force data from the -o .trr option to trjconv.
>>
>> Chris
>>
>>
>>
>> --- Original Message ---
>>
>> Hi,
>> I think after the "trjconv -f *.trr -n deshuf.ndx" operation,  the new 
>> or=
>> ders of x and v in the trr file are correct.=20
>> Here "correct" means the order is the same as the intitial *.gro file 
>> you=
>> use for grompp command. If the output
>> of trjconv is gro/pdb, you're right that it's only deshuffled, but not 
>> de=
>> sorted. But since there's no force in the gro
>> file, the bug i mentioned is only in the case when you choose trr as 
>> the =
>> output of your deshuffle operation.
>> Lanyuan Lu
>> 
>>> / Date: Thu, 24 Jan 2008 12:28:47 -0500
>> />/ From: chris.neale at utoronto.ca 
>> 
>> />/ To: gmx-users at gromacs.org 
>> 
>> />/ Subject: [gmx-users] deshuf.ndx doesn't work for forces?
>> />/=20
>> />>/ Message: 2
>> />>/ Date: Wed, 23 Jan 2008 18:56:22 -0500
>> />>/ From: LuLanyuan=20
>> />>/ Subject: [gmx-users] deshuf.ndx doesn't work for forces?
>> />>/ To:=20
>> />>/ Message-ID:=20
>> />>/ Content-Type: text/plain; charset=3D"gb2312"
>> />>/
>> />>/
>> />>/ Hello All,
>> />>/ I found sth like a bug regarding the deshuffle index file. I did 
>> a  =20
>> />>/ simulation using multiple cpus and -sort -shuffle options. After  
>> =20
>> />>/ that I tried to use the deshuf.ndx file to recover the original 
>> atom =20
>> />>/  order for my trr file by trjconv -n deshuf.ndx ... command.
>> />/=20
>> />/ As I understand it, the deshuf.ndx file does not allow you to 
>> desort, =20
>> />/ merely to deshuffle.
>> />/=20
>> />>/ But by checking the output trr using the gmxdump, I found the 
>> oders =20
>> />>/ of x  and v were deshuffled while the f oder remained unchanged. 
>> In  =20
>> />>/ another word the values of forces were not consistent with those 
>> of  =20
>> />>/ positions and velocities in the new trr file.
>> />>/ Is this a bug?
>> />/=20
>> />/ So the order of the positions and velocities has changed, but are 
>> they =
>> /=20
>>> / correct? I do not believe that gromacs 3.3.1 is capable of 
>>> desorting, =20
>> />/ nor is it supported. I have uploaded a tool called g_desort to the 
>> =20
>> />/ users contribution section. It works well and is tested, but it's =20
>> />/ usage is complicated when you want to load in .trr files via grompp.
>> />/=20
>> />>/ And is there anyway to get the correct oder for forces also?
>> />/=20
>> />/ I suggest that you try to reproduce this problem while using 
>> -shuffle =20
>> />/ but not -sort.
>> />/=20
>> />>/ Thanks a lot.
>> />>/ Lanyuan Lu/
>>
>>
> 
> 

[gmx-users] genbox memory problem

[LuLanyuan]

Hello,
I have a problem about genbox command in GMX. I'm running genbox to randamly 
insert molecules. Because the probobility of successful insertion is low, I 
have to use a large number for the "-try" variable. After running genbox I 
found sometimes the memory cost increased gradually after each unsuccessful 
inserion attempt and finally went beyond the limit of hardware. The memory cost 
went back to a very small number after one successful insertion. I'm wondering 
if it's a memory leakage problem. In my unsterstanding the memory cost 
shouldn't increase after each unsuccessful insertion.  Is that because some 
momeory is not freed after each try?
Thanks.
Lanyuan Lu
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RE: [gmx-users] g_wham command issues

[LuLanyuan]

I remember that at least for the old version of g_wham, you need to gzip the 
pdo files first.
Lanyuan Lu


> Date: Tue, 1 Jul 2008 11:38:18 -0400
> To: gmx-users@gromacs.org
> From: [EMAIL PROTECTED]
> Subject: [gmx-users] g_wham command issues
> 
> Hello,
> 
> I am having trouble analyzing the XXX.pdo file output from my mdrun 
> simulation using the g_wham command.  Specifically, my command entered is:
> 
> g_wham pull.pdo -o pull1.xvg
> 
> The error given is:
> 
> Opening file pull.pdo
> _
> Program g_wham, VERSION 3.3.3
> Source code file: gmx_wham.c, line 89
> 
> Fatal error:
> This does not appear to be a valid pdo file
> _
> 
> "Motherhood Means Mental Freeze" (The Breeders)
> 
> 
> I've looked into the gmx_wham.c file and found that line 89 corresponds to:
> 
> if(strcmp(Buffer1,"UMBRELLA"))
> fatal_error( 704 ,"This does not appear to be a valid pdo file");
> 
> 
> I'm not sure of what this means.  I've noticed that others have had this 
> issue in the past, and am hoping someone has found my mistake.  Formatting of 
> my .pdo file maybe?  If this is the case, can anyone provide sample .pdo file 
> to compare with my own?  Any help is appreciated.
> __
> 
> Venkatesh Hariharan
> Pennsylvania State University
> Schreyer Honors College
> Undergraduate - Bioengineering
> 
> "You must be the change you wish to see in the world."
> --Mohandas Karamchand Gandhi

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[gmx-users] What's the default pbc of Gromacs trajectories?

[LuLanyuan]

Hello,
I just noticed the -pbc option for the trjconv command had changed after a 
version 3.3.x.
The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc.
As I remember for early versions of Gromacs the default pbc of output 
trajectories was "whole",
which means no broken molecules. But I just found it's not the case for the 
latest version, since
I can see broken lipids for my membrane system using "ngmx". I'm just wondering 
what's the
default pbc for the latest Gromacs version and whether there is a way to change 
it before MD
simulations.
Thanks for your help.
Lanyuan Lu
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RE: [gmx-users] What's the default pbc of Gromacs trajectories?

[LuLanyuan]

Thanks for your reply. I just checked the online manual for .mdp. But I didn't 
find
an option to change output pbc types. If I need the output trr file to be 
"whole" as
that from an older version, can I set it up anywhere?
I understand I can use trjconv to convert trr files. But usually trr files are 
huge and
the convertion takes time.
Thanks,
Lanyuan Lu

> Date: Mon, 28 Jul 2008 17:07:30 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories?
> 
> 
> 
> LuLanyuan wrote:
> > Hello,
> > I just noticed the -pbc option for the trjconv command had changed after a 
> > version 3.3.x.
> > The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc.
> > As I remember for early versions of Gromacs the default pbc of output 
> > trajectories was "whole",
> > which means no broken molecules. But I just found it's not the case for the 
> > latest version, since
> > I can see broken lipids for my membrane system using "ngmx". I'm just 
> > wondering what's the
> > default pbc for the latest Gromacs version and whether there is a way to 
> > change it before MD
> > simulations.
> 
> I think you are asking two separate questions.
> 
>  From trjconv -h you can find the default behavior for PBC treatment, which 
> is 
> "none," as in, leave the coordinates alone.
> 
> The PBC behavior of an MD simulation is specified in the .mdp file.  Removal 
> of 
> PBC from "broken" starting structures should be the first step in the 
> simulation.
> 
> -Justin
> 
> > Thanks for your help.
> > Lanyuan Lu
> > _
> > MSN 中文网，最新时尚生活资讯，白领聚集门户。
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> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> 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] A bug of trjconv for force output?

[LuLanyuan]

Hello All,
I just found a strange problem for the gromacs tool trjconv. I have a 
trajectory (and the tpr file) which contains three groups of molecules and x,v 
and f. When I use trjconv to output the trajectory of the 1st group, everything 
is fine. For example, I have A,B and C groups in my trajectory and I choose A 
only at the prompt of trjconv and use "-force" option to include forces in my 
output trajectory of A only. But if I want a trajectory of C only, I found the 
output forces were wrong. Positions and velocities are right in this case. It 
seems to me the trjconv just pick the first N force numbers to write where N is 
the total number of atoms in group C. In fact these forces belong to group A 
and B. This "logic" of trjconv explains why the output is correct if I choose 
the first group A to write.
Some month ago I reported a problem regarding the deshuf.ndx and the wrong 
force output. I think that problem is related to this problem. Because fewer 
people use forces, I think this is the reason these bugs haven't been found 
before. I appreciate if some authors can fix them.
Thanks.
Lanyuan Lu 
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RE: [gmx-users] cgnr

[LuLanyuan]

Hi Lin,
Please read the manual. By checking the "Index" section you'll find charge 
group.
For example, there is a paragraph in page 20.
Lanyuan Lu


> Date: Thu, 21 Aug 2008 09:52:35 -0700
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] cgnr
> 
> Hi
> As Justin described,
> cgnr = charge group number
> 
> could anyone explain more about this ?
> and, how to determin cgnr?
> 
> Thanks
> Lin
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[gmx-users] PME problem on BG/P cluster

[LuLanyuan]

Hello,
I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" at 
Argonne national lab).
The simulated system is a box of SPC water with 648,000 atoms and all MD 
simulations were performed on 256 CPU cores with MPI. The compiling environment 
was Linux with IBM compiler and libs.
I first compile the code with flags suggested on the Wiki, such as:
./configure --prefix=$PREFIX \
   --host=ppc \
   --build=ppc64 \
   --disable-software-sqrt \
   --enable-ppc-sqrt=1 \
   --enable-ppc-altivec \
   --enable-bluegene \
   --disable-fortran \
   --enable-mpi \
   --with-fft=fftpack \
   --without-x \
   CC="mpixlc_r" \
   CFLAGS="-O3 -qarch=450d -qtune=450" \
   MPICC="mpixlc_r"
   CXX="mpixlcxx_r"
   CXXFLAGS="-O3 -qarch=450 -qtune=450"
   F77="mpixlf77_r"
   FFLAGS="-O3 -qarch=450 -qtune=450"
   LIBS="-lmass"

Here I used fftpack to ensure that the problem is not due to the fftw lib. I 
got the water system running will with Cut-off for electrostatics. However, the 
systems always crashed after a few ( ~100) steps if I used PME. The same system 
with same PME option runs fine on other non-blue gene clusters I tested. 
The error message I got was sth like 
t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates.

and

2 particles communicated to PME node 63 are more than a cell length out of the 
domain decomposition cell of their charge group

>From .log file, the kinetic energy is increasing and turned to be "nan". So 
>the system is exploding.

I found if I turned off the blue gene optimizations during configure, the water 
system could be run without problem. For example, I used
   --enable-software-sqrt \

   --disable-ppc-sqrt \

   --disable-bluegene \
and everything else was the same. 
I suspect there was an issue regarding the blue gene specific code and PME.
Could anyone give any comments?

Thanks a lot.
Lanyuan Lu
  
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RE: [gmx-users] PME problem on BG/P cluster

[LuLanyuan]

Hi, 
Thanks for all the suggestions.
Actually I also tried it without the ativec flag (using the same flags as those 
on the wiki) and the outcome was the same.
I did test it with the fftw3 officially installed on the cluster, and got the 
same error. Because the problem is related to PME, my first guess is that it 
may due to fftw and then tried it with fftpack. However, I also did many tests 
with fftw-3 and got similar results.
Thanks,
Lanyuan Lu 

> Date: Fri, 4 Jun 2010 19:32:45 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] PME problem on BG/P cluster
> 
> On 2010-06-04 17.49, LuLanyuan wrote:
> > Hello,
> > I got a weird problem by running Gromacs 4.0.7 on a BG/P machine 
> > ("Intrepid" at Argonne national lab).
> > The simulated system is a box of SPC water with 648,000 atoms and all MD 
> > simulations were performed on 256 CPU cores with MPI. The compiling 
> > environment was Linux with IBM compiler and libs.
> > I first compile the code with flags suggested on the Wiki, such as:
> > ./configure --prefix=$PREFIX \
> > --host=ppc \
> > --build=ppc64 \
> > --disable-software-sqrt \
> > --enable-ppc-sqrt=1 \
> > &n bsp; --enable-ppc-altivec \
> > --enable-bluegene \
> > --disable-fortran \
> > --enable-mpi \
> > --with-fft=fftpack \
> > --without-x \
> > CC="mpixlc_r" \
> > CFLAGS="-O3 -qarc h=450d -qtune=450" \
> > MPICC="mpixlc_r"
> > CXX="mpixlcxx_r"
> > CXXFLAGS="-O3 -qarch=450 -qtune=450"
> > F77="mpixlf77_r"
> > FFLAGS="-O3 -qarch=450 -qtune=450"
> > LIBS="-lmass"
> > 
> > Here I used fftpack to ensure that the problem is not due to the fftw 
> > lib. I got the water system running will with Cut-off for 
> > electrostatics. However, the systems always crashed after a few ( ~100) 
> > steps if I used PME. The same system with same PME option runs fine on 
> > other non-blue gene clusters I tested.
> > The error message I got was sth like
> > t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.
> > Check for bad contacts and/or reduce the timestep.
> > Wrote pdb files with previous and current coordinates.
> > 
> > and
> > 
> > 2 particles communicated to PME node 63 are more than a cell length out 
> > of the domain decomposition cell of their charge group
> > 
> >  From .log file, the kinetic energy is increasing and turned to be 
> > "nan". So the system is exploding.
> > 
> > I found if I turned off the blue gene optimizations during configure, 
> > the water system could be run without problem. For example, I used
> > --enable-software-sqrt \
> > --disable-ppc-sqrt \
> > --disable-bluegene \
> > and everything else was the same.
> > I suspect there was an issue regarding the blue gene specific code and PME.
> > Could anyone give any comments?
> >
> I would strongly suggest to use FFTW3.
> All other FFT libraries are not so well tested.
> 
> -- 
> 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
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] PME problem on BG/P cluster

[LuLanyuan]

Dear Mark,
When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any 
problem. So I guess it's related to the assembly loops for BG.
Thanks,
Lanyuan


From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Sat, 5 Jun 2010 03:31:33 +1000
Subject: Re: [gmx-users] PME problem on BG/P cluster



- Original Message -
From: LuLanyuan 
Date: Saturday, June 5, 2010 2:01
Subject: [gmx-users] PME problem on BG/P cluster
To: gmx-users@gromacs.org

   >  Hello,
> I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" 
> at Argonne national lab).
> The simulated system is a box of SPC water with 648,000 atoms and all MD 
> simulations were performed on 256 CPU cores with MPI. The compiling 
> environment was Linux with IBM compiler and libs.
> I first compile the code with flags suggested on the Wiki, such as:
> ./configure --prefix=$PREFIX \
>--host=ppc \
>--build=ppc64 \
>--disable-software-sqrt \
>--enable-ppc-sqrt=1 \
> &n  bsp;  --enable-ppc-altivec \


The wiki doesn't suggest this, and it's for another architecture entirely. I 
don't know if it's causing a problem, but you should see what kernels the .log 
file reports it is trying to use.


>--enable-bluegene \
>--disable-fortran \
>--enable-mpi \
>--with-fft=fftpack \


This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for 
BlueGene. [Edit: ah I see why you tried this]


>--without-x \
>CC="mpixlc_r" \
>CFLAGS="-O3 -qarc  h=450d -qtune=450" \
>MPICC="mpixlc_r"
>CXX="mpixlcxx_r"
>CXXFLAGS="-O3 -qarch=450 -qtune=450"
>F77="mpixlf77_r"
>FFLAGS="-O3 -qarch=450 -qtune=450"
>LIBS="-lmass"
> 
> Here I used fftpack to ensure that the problem is not due to the fftw lib. I 
> got the water system running will with Cut-off for electrostatics. However,   
> the systems always crashed after a few ( ~100) steps if I used PME. The same 
> system with same PME option runs fine on other non-blue gene clusters I 
> tested. 
> The error message I got was sth like 
> t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates.
> 
> and
> 
> 2 particles communicated to PME node 63 are more than a cell length out of 
> the domain decomposition cell of their charge group
> 
> From .log file, the kinetic energy is increasing and turned to be "nan". So 
> the system is exploding.
> 
> I found if I turned off the blue gene optimizations during configure, the 
> water system could be run without problem. For example, I used
>--enable-software-sqrt \
> --disable-ppc-sqrt \
> --disable-bluegene \
> and everything else was the same. 
> I suspect there was an issue regarding the blue gene specific code and PME.
> Could anyone give any comments?


First, try without --enable-ppc-altivec in case that's confusing things. Then 
try setting the enviroment variable NOASSEMBLYLOOPS to 1 before mdrun to see 
whether the issue really is specific to the BlueGene-kernel. (Consult mpirun 
documentation about how to set env vars suitably) You might also try compiling 
with lower optimization levels, to see if its a compiler/optimization issue. 
Depending what you find above, there are other things to try.



Mark

  
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RE: [gmx-users] PME problem on BG/P cluster

[LuLanyuan]

Thanks, Mark. I've post it on the bugzilla. I'm glad to try the new assembly 
loops on BG/P as well.
Lanyuan

From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Wed, 9 Jun 2010 07:48:26 +1000
Subject: Re: RE: [gmx-users] PME problem on BG/P cluster

- Original Message -----
From: LuLanyuan 
Date: Wednesday, June 9, 2010 2:10
Subject: RE: [gmx-users] PME problem on BG/P cluster
To: gmx-users@gromacs.org

   >  Dear Mark,
> When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any 
> problem. So I guess it's related to the assembly loops for BG.

OK, that's useful data. I understand that these loops are believed to work on 
BG/P. Knowing the code, I can think of no reason why the problem should be 
BG/P-specific. Please open a http://bugzilla.gromacs.org report, CC my email 
address, and attach your .tpr, and I'll try it on my BG/L.

I actually have well-tested ready-to-release updates to these kernels that 
perform up to about 10% better on PME on BG/L. Depending what we find above, 
and if you're interested, I could let you try them on BG/P, since I don't have 
the ability to test on BG/P.

Mark

> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Date: Sat, 5 Jun 2010 03:31:33 +1000
> Subject: Re: [gmx-users] PME problem on BG/P cluster
> 
> 
> 
> - Original Message -
> From: LuLanyuan 
> Date: Saturday, June 5, 2010 2:01
> Subject: [gmx-users] PME problem on BG/P cluster
> To: gmx-users@gromacs.org
> 
>> >  Hello,
> > I got a weird problem by running Gromacs 4.0.7 on a BG/P machine 
> > ("Intrepid" at Argonne national lab).
> > The simulated system is a box of SPC water with 648,000 atoms and all MD 
> > simulations were performed on 256 CPU cores with MPI. The compiling 
> > environment was Linux with IBM compiler and libs.
> > I first compile the code with flags suggested on the Wiki, such as:
> > ./configure --prefix=$PREFIX \
> >--host=ppc \
> >--build=ppc64 \
> >--disable-software-sqrt \
> >&  nbsp;   --enable-ppc-sqrt=1 \
> > &n  bsp;  --enable-ppc-altivec \
> 
> 
> The wiki doesn't suggest this, and it's for another architecture entirely. I 
> don't know if it's causing a problem, but you should see what kernels the 
> .log file reports it is trying to use.
> 
> 
> >--enable-bluegene \
> > &n  bsp;  --disable-fortran \
> >--enable-mpi \
> >--with-fft=fftpack \
> 
> 
> This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for 
> BlueGene. [Edit: ah I see why you tried this]
> 
> 
> >--wit  hout-x \
> > &nbs p;  CC="mpixlc_r" \
> >CFLAGS="-O3 -qarc  h=450d -qtune=450" \
> >MPICC="mpixlc_r"
> >CXX="mpixlcxx_r"
> >CXXFLAGS="-O3 -qarch=450 -qtune=450"
> >F77="mpixlf77_r"
> >FFLAGS="-O3 -qarch=450 -qtune=450"
> >LIBS="-lmass"
> > 
> > Here I used fftpack to ensure that the problem is not due to the fftw lib. 
> > I got the water system running will with Cut-off for electrostatics. 
> > However,   the systems always crashed after a few ( ~100) steps if I used 
> > PME. The same system with same PME option runs fine on other non-blue gene 
> > clusters I tested. 
> > The error message I got was sth like 
> > t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.
> > Check for bad contacts and/or reduce the timestep.
> > Wrote pdb files with previous and current coordinates.
> > 
> > and
> > 
> > 2 particles communicated to PME node 63 are more than a cell length out of 
> > the domain decomposition cell of their charge group
> > 
> > < /font>From .log file, the kinetic energy is increasing and turned to be 
> > "nan". So the system is exploding.
> > 
> > I found if I turned off the blue gene optimizations during configure, the 
> > water system could be run without problem. For example, I used
> >--enable-software-sqrt \
> > -  -disable-ppc-sqrt \
> > --disable-bluegene \
> > and everything else was the same. 
> > I suspect there was an issue regarding the blue gene specific code and PME.
> > Could anyone give any comments?
> 
> 
>

RE: [gmx-users] g_wham

[LuLanyuan]

Hi, 
I don't remember whether the bug has been fixed for 3.3.*. Can any gromacs guy 
clarify that?
Abu, have you tried the original g_wham first? If it really dosen't work, 
please shoot me an email. 
Then I can send you the correct file.
Lanyuan Lu






> Date: Fri, 14 Sep 2007 14:41:23 +0100> From: 
[EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: [gmx-users] g_wham>> 
Hi,> Is there any way I can get corrected version of g_wham? I know form the 
discussion archive> that David Bostick has a copy of the corrected g_wham.> 
With regards,> Abu Naser> School Of Life Sciences> Heriot-Watt University> 
Edinburgh EH14 4AS> Email: [EMAIL PROTECTED]> Phone: +44(0)1314518265> Fax : 
+44(0) 131 451 3009

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