[gmx-users] Is openmp necessary?

2011-12-09 Thread Hsin-Lin Chiang 

Hi,

For mdrun, the option -nt means "Number of threads to start (0 is guess)".
Is this option executed by openmp?
I used this option every time.
But today my technology stuff told me that we don't have openmp 
installed in our computer.

It make me confused.
Why can I compile and run mdrun -nt 12 before?

Sincerely yours,
Hsin-Lin
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Re: [gmx-users] Is openmp necessary?

2011-12-09 Thread Mark Abraham 

On 9/12/2011 7:48 PM, Hsin-Lin Chiang wrote:

Hi,

For mdrun, the option -nt means "Number of threads to start (0 is 
guess)".

Is this option executed by openmp?
I used this option every time.
But today my technology stuff told me that we don't have openmp 
installed in our computer.

It make me confused.
Why can I compile and run mdrun -nt 12 before?


mdrun does not use OpenMP at all. -nt creates standard threads, for 
which the best performance will normally be one per physical core, which 
will be auto-detected if you don't specify -nt.


Mark
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[gmx-users] Re: Is openmp necessary?

2011-12-09 Thread Hsin-Lin Chiang 

Hi Mark,

Thank you for your reply.
I understand now.

Sincerely yours,
Hsin-Lin

I want to calculate the diffusion coefficient of a small polypeptide
with g_msd (see here
http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)

because of periodic boundary condition, when the peptide goes out of
the right side it comes in from left side, which leads to an
artificial displacement. this will give rise to a non-realistic MSD.

is g_msd intelligent enough to avoid this artificial displacement?


Yes it is.


Not sure about g_msd, but you can take care of it yourself with a
workflow derived from the information here
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


Mark




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[gmx-users] Fwd: Check for bad contacts and/or reduce the timestep

2011-12-09 Thread Mark Abraham 

Hi,

Please keep such discussions on the mailing list so that others can 
learn and contribute from the discussion and its archive.


On point, this .mdp file has a feature about which I have already 
indicated a link that highlights its undesirability. Moreover, this .mdp 
file did not produce the simulation that crashed, because you've 
previously reported the same output from a different .mdp file. That 
kind of mismatch makes it hard for people to want to help...


The link Justin provided originally has tips on how to diagnose what is 
going wrong on systems that are blowing up. You should read that link 
and follow links from it. In the absence of new information from you, 
there's really nothing else that we can help with.


Mark

 Original Message 
Subject:Check for bad contacts and/or reduce the timestep
Date:   Fri, 09 Dec 2011 13:28:41 +0530
From:   pragna lakshmi 
To: mark.abra...@anu.edu.au



Dear Mark,
  i am trying to do protein-ligand simulation. while 
running energy minimization step maximum force is on atom 2099. And it 
was completed in 696 steps. I used pr.mdp file for equilibration which 
is given below.


title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
Pcoupl = no
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529

  pr.mdp step run well. But at 
final md step it is showing the following error.


Step 105692, time 211.384 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002880, max 0.071917 (between atoms 2097 and 2095)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2098   2099   38.60.1330   0.1371  0.1330
   2097   2098   45.20.1330   0.1370  0.1330
.
.
.
.
Step 226039, time 452.078 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 42.444550, max 1059.016235 (between atoms 2098 and 2099)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2095   2094   31.60.1441  10.5310  0.1250
   2113   2114   40.80.1471   0.1950  0.1470
   2117   2112   36.40.1521   0.1902  0.1520
   2111   2113   81.70.1535   0.2949  0.1520
   2111   2112   83.90.1534   0.2900  0.1520
   2111   2110  113.20.1833   0.8261  0.1780
   2109   2110   43.80.2063  11.5418  0.1750
   2107   2109   38.30.1516  11.2487  0.1390
   2107   2108  103.00.1581  11.5450  0.1530
   2106   2107   77.40.1333  30.0780  0.1530
   2104   2105  140.00.1080   2.2354  0.1000
   2102   2104   34.20.1426  16.8737  0.1430
   2102   2103   89.90.1637  15.4076  0.1530
   2101   2106  142.00.2077  63.6808  0.1530
   2101   2102  132.50.1659  62.8960  0.1530
   2101   2099  174.70.5646 127.3807  0.1390
   2099   2100  160.10.5219 101.4140  0.1230
   2106   2098  166.30.2022  76.2729  0.1480
   2098   2099  174.80.6156 140.9822  0.1330
   2097   2109  149.50.1057  36.9859  0.1330
   2097   2098  159.40.2818  84.7773  0.1330
   2097   2095  164.80.1042  37.0501  0.1330
   2095   2096   70.70.1482   9.8470  0.1250
Wrote pdb files with previous and current coordinates
There were 4 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 2094 and 2098 at distance 44.117 which 
is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
.
.
.
.
   1416   1417   89.70.1530 705915256832.  0.1530
   1414   1416   90.40.1470 419510747136.  0.1470
   1414   1415   92.30.1000 45284384768.  0.1000
   1412   1414   89.50.1330 55051784192.  0.1330
   1412   1413  106.40.1230 13457604608.  0.1230
   1409   1411  119.20.1530 519590400.  0.1530
   1409   1410  107.40.1530 519590400.  0.1530
   1408   1412   99.10.1530 14933683200.  0.1530
   1408   1409   98.30.1530 4102264576.  0.1530

[gmx-users] Gromos parameters for atom type OA

2011-12-09 Thread Samuli Ollila 
Dear all,

I was comparing Gromos 45a3 and 53a6 force fields and I found something which I 
cannot understand. The atom type OA is described in  ffG45a3nb.itp as:
;name  at.num   mass  charge  ptype  c6   c12
OA8 0.000  0.000 A  0.0022619536  1.505529e-06
 and in ffG53a6nb.itp:
OA8 0.000  0.000 A  0.0022619536  1.505529e-06
which are same parameters.

However, according to Gromos developers the atom type OA has been changed 
between Gromos 45a3 and 53a6. The parameters given by Gromos developers for 
45a3 are
#   IAC TYPESQRT(C6)   SQRT(C12(1))  SQRT(C12(2)) SQRT(C12(3))
  3   OA  0.04756 1.1250E-3   1.227E-30.0
and for 53a6
  3  OA 0.04756 1.100E-3 1.227E-3 0.0

The actual numbers are different for parameters used in Gromacs since the way 
to write parameters is different.

My problem is that there is difference in OA type between 45a3 and 53a6 in 
parameters given by Gromos developers but not in the files distributed in 
Gromacs package. Can someone explain this?

BR,
Samuli Ollila
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[gmx-users] Re: gmx-users Digest, Vol 92, Issue 49

2011-12-09 Thread Sławomir Stachura 
Ah, OK. The commands I used were:

g_msd -n POPC_index.ndx  -lateral z -o POPC_150ns_CM_MSDlat.xvg -mol diffmol.xvg
g_msd -n POPC_index.ndx  -lateral z -o POPC_150ns_MW_MSDlat.xvg


> 
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> --
> 
> Message: 2
> Date: Fri, 09 Dec 2011 12:36:49 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] Re:Re:Re: MSD normalization
> To: Discussion list for GROMACS users 
> Message-ID: <4ee16631.2030...@anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> On 9/12/2011 5:37 AM, Sławomir Stachura wrote:
>> Hi!
>> Thanks Mark for reply. When I calculated fractional diffusion constant from 
>> mass weighted MSD of long simulation I get sth about 0.05. But when I do the 
>> same for centre of mass, considering that MSD is expressed in nm^2, the 
>> result is 1.35. When I look into xvg file  MSD of centre of mass is 10-20 
>> times than for mass-weighted (which is substantially wrong). So assuming 
>> that, by any chance, centre of mass MSD is in A^2, calculated fractional 
>> diffusion constant is of 0.02 magnitude, which is theoretically more 
>> understandable.
>> What I can show you is a sample of two MSDs:
>> 
>> - Mass weighted:
>> 
>>  0   0
>> 15   0.0150352
>> 30   0.0198877
>> 45   0.0235849
>> 60   0.0267214
>> 75   0.0294651
>> 90   0.0319853
>>105   0.0342538
>>120   0.0364239
>>135   0.0384275
>>150   0.0403661
>>165   0.0421938
>>180   0.0439495
>>195   0.0456557
>>210   0.0472885
>>225   0.0488768
>>240   0.0503814
>>2550.051868
>>270   0.0533207
>>285   0.0547436
>>300   0.0561625
>> 
>> -And centre of mass:
>> 
>>  0   0
>> 150.916885
>> 30 1.05944
>> 45 1.16649
>> 60 1.25004
>> 75 1.31444
>> 90 1.37307
>>105 1.43301
>>120 1.47879
>>135 1.52776
>>150 1.57137
>>165  1.6211
>>180 1.64439
>>195 1.68883
>>210 1.71222
>>225 1.75035
>>240 1.77255
>>255  1.8117
>>270 1.83702
>>285 1.87376
>>300  1.8958
>> 
>> 
>> But still there is more thing - do you how the MSD is normalized? Because I 
>> have compared mass weighted MSD calculated using Gromacs tool and nMoldyn 
>> and I get the same difference for all my cases (simulations of 2ns, 15ns and 
>> 150ns)- in the latter  diffusion constant is twice the value of the one 
>> obtained in Gromacs. So I expect the difference in normalization.
> 
> OK, but we need to see your terminal command lines in order to eliminate 
> your use of the tool as a source of the problem. They should be at the 
> top of the .xvg file, if nowhere else.
> 
> Mark
> 
>> 
>> Cheers,
>>Slawomir
>> 
>> 
>> 
>> 
>>> On 6/12/2011 3:58 AM, S“awomir Stachura wrote:
 Hi,
 
 There is something interesting concerning these MSD calculations. If I 
 treat Centre of Mass MSD  if it'd be expressed not in nm^2/ps , but 
 Angstroms^2/ps, I get ideally the same results as for mass-weighted ones. 
 And it's true for all my three cases, in which I performed simulation of 
 different times. Is that possible there is some bug in MSD? Because as for 
 me it looks so
>>> I would be amazed if GROMACS did this. Can you copy and paste from your
>>> terminal to show this?
>>> 
>>> Mark
>>> 
 Hope to have someone join the discussion,
Slawomir
 
 
 
 
 
 Wiadomo¶æ napisana przez S“awomir Stachura w dniu 2011-12-04, o godz. 
 22:38:
 
> Hi,
> 
> I was just wondering how MSDs in Gromacs are normalized. I am 
> calculatiing MSDs for my lipid system of different timesteps of 
> simulation and I get much higher results for centre of mass calculations 
> in comparison to mass-weighted one.  And I thought about normalization 
> issue, but I couldn't find any informations concerning that topic in 
> manual.
> I'd be grateful if someone could explain how mean square displacement is 
> normalized.
> 
> Cheers,
>   Slawomir
> 

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[gmx-users] gromacs/orca--qmmm

2011-12-09 Thread li yan 
Dear Gromacs developers:
I'm trying to run a QM-MM single point energy calculation on a
structure (a small molecule with 50 water molecules with no pbc, no
cutoff). I use orca for QM part amd gromacs for MM part. But when I
run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly
and terminate naormally, but after that mdrun run stops with a
segmentation fault. Here is the error information: *Back Off! I just
backed up sp.log to ./#sp.log.1#**Reading file sp.tpr, VERSION 4.5.5
(single precision)**QM/MM calculation requested.**there we go!**Layer
0**nr of QM atoms 9**QMlevel: MP2/3-21G*
*/home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360...**orca
initialised...*
*Back Off! I just backed up traj.trr to ./#traj.trr.1#*
*Back Off! I just backed up ener.edr to ./#ener.edr.1#**starting mdrun
'Protein'**0 steps,  0.0 ps.**Calling
'/home/li/programs/orca_x86_64_exe_r2360/orca
/home/li/Test/test_gmx/qmmm/test/sp.inp >>
/home/li/Test/test_gmx/qmmm/test/sp.out'**Segmentation fault*

Here is my sp.mdp
title= test
cpp  =/lib/cpp
integrator   = md
nsteps   = 0
dt   = 0.001
;constraints = none
emtol= 10.0
emstep   = 0.01
nstcomm  = 1
ns-type  = simple
nstlist  = 0
rlist= 0
rcoulomb = 0
rvdw = 0
tcoupl   = no
pcoupl   = no
gen-vel  = no
nstxout  = 1
nstlog   = 1
nstenergy= 1
nstvout  = 1
nstfout  = 1
pbc  = no
comm_mode= angular
; non-equilibrium md
freezegrps   = System
freezedim= y y y
xtc_grps = System
energygrps   = System
;qmmm calculation
QMMM = yes
QMMM-grps= QMatoms
QMMMscheme   = normal
QMmethod = MP2
QMbasis  = 3-21g
QMcharge = 0
QMmult   = 1
The *.ORCAINFO is:
 *! RKS b3lyp/g sv(p) tightscf*
And I also tried QMMMsheme=ONIOM, but I get the segmentation fault
too. Am I missing something in all of this?  Any help would be highly
appreciated.
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Re: [gmx-users] Gromos parameters for atom type OA

2011-12-09 Thread Javier Cerezo 
GROMOS force field builds the LJ parameters by multiplication of the 
square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12) 
labels). In the case of the repulsion term (C12), up to three of such 
parameters are possible:  SQRT(C12(1))  SQRT(C12(2)) SQRT(C12(3)), when 
combined with other atoms, depending on the desired repulsion strength 
(e.g. the enhanced C12(3) repulsion is used to keep charged groups 
separated). Which of the three is used depends on the combination of 
atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15 
in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or 
in the ifp file the last lines for each atom type containing "1", "2" 
and "3"). For the case of OA, this matrix specifies that the second C12 
term is to be used when OA encountes another OA. So, according, to the 
ifp line you showed:


C12(OA-OA) =  SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 = 
1.50553E-6


Which is the same for 45a3 and 54a6 force fields.

Differences in the parameters will show up only in the cases where the 
SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2))


Javier

El 09/12/11 16:12, Samuli Ollila escribió:

Dear all,

I was comparing Gromos 45a3 and 53a6 force fields and I found 
something which I cannot understand. The atom type OA is described in  
ffG45a3nb.itp as:

;name  at.num   mass  charge  ptype  c6   c12
OA8 0.000  0.000 A  0.0022619536  1.505529e-06
 and in ffG53a6nb.itp:
OA8 0.000  0.000 A  0.0022619536  1.505529e-06
which are same parameters.

However, according to Gromos developers the atom type OA has been 
changed between Gromos 45a3 and 53a6. The parameters given by Gromos 
developers for 45a3 are

#   IAC TYPESQRT(C6)   SQRT(C12(1))  SQRT(C12(2)) SQRT(C12(3))
  3   OA  0.04756 1.1250E-3   1.227E-30.0
and for 53a6
  3  OA 0.04756 1.100E-3 1.227E-3 0.0

The actual numbers are different for parameters used in Gromacs since 
the way to write parameters is different.


My problem is that there is difference in OA type between 45a3 and 
53a6 in parameters given by Gromos developers but not in the files 
distributed in Gromacs package. Can someone explain this?


BR,
Samuli Ollila




--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434

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[gmx-users] Problem with GDP parameters generation

2011-12-09 Thread neeru sharma 
Dear gromacs users,

I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving
unreliable output, I generated Amber topology and coordinate files for GTP
molecule. Then, I converted them into the corresponding gromacs topology
(.top) and coordinate files (.gro) and generated parameter (.itp) file
using following command (Thanks to Tsjerk):
sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p'
TOP > ITP

But the topology and co-ordinates file are quite different from the input
PDB file and hence the parameters are also faulty, the GDP molecule is not
fitting in the binding pocket of protein. Upon tracking the whole process,
it was found that the error might be while using antechamber for generating
prepin file using Gaussian output file as the input.

Can anyone please suggest some way to apply some constraints in the
antechamber command itself. OR if anybody has the paramters or topology for
GDP, can anyone provide me the same so that I can compare and see where the
parameters are differing.

Thanks


Neeru Sharma
Pune (India)
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[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

2011-12-09 Thread Ruhollah Moussavi-Baygi 
David,
thank you for your reply.

but, g_msd gives a diffusion coefficient which is one order of magnitude
higher than expected for a small polypeptide (15 res long with gyration Rg
~ 0.8nm) with the same size. this is command line i used:
g_msd-mpi -f  md_mine_2nd.xtc -s  md_mine_2nd.tpr -o  msd_2nd.xvg

when visualizing, I can see that the polypeptide crosses the boundary
several times. apparently,  g_msd counts these 'artificial' jumps in MSD
calculation.  and, that's probably why the diffusion coefficient is
calculated such high (i.e. 500 um2/s for a small protein).

if this is the case, it is a bug in g_msd I believe.

is there any way to get round this problem?

-- Forwarded message --
From: Anonymous 
Date: Fri, Dec 9, 2011 at 12:17 AM
Subject: Comment for Forum topic: diffusion coefficient
To: ruhollah...@gmail.com


Hi ruhollahmoussavi-baygi,

Comment by davidvanderspoel: diffusion coefficient


On 2011-12-09 08:34, Mark Abraham wrote:
> On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
>> I want to calculate the diffusion coefficient of a small polypeptide
>> with g_msd (see here
>> http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constant[1])
>>
>> because of periodic boundary condition, when the peptide goes out of
>> the right side it comes in from left side, which leads to an
>> artificial displacement. this will give rise to a non-realistic MSD.
>>
>> is g_msd intelligent enough to avoid this artificial displacement?
>>
>
Yes it is.


> Not sure about g_msd, but you can take care of it yourself with a
> workflow derived from the information here
> http://www.gromacs.org/**Documentation/Terminology/**
Periodic_Boundary_Condi...
[2]
>
>
> Mark

Read more http://support.scalalife.eu/**content/diffusion-coefficient#**
comment-103


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[1] 
http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constant
[2] http://www.gromacs.org/**Documentation/Terminology/**
Periodic_Boundary_Conditions




-- 
Best,
Ruhollah Moussavi-Baygi
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Re: [gmx-users] Problem with GDP parameters generation

2011-12-09 Thread Mark Abraham 

On 10/12/2011 6:25 AM, neeru sharma wrote:

Dear gromacs users,

I have to simulate a protein-GDP complex using gromacs.As PRODRG was 
giving unreliable output, I generated Amber topology and coordinate 
files for GTP molecule. Then, I converted them into the corresponding 
gromacs topology (.top) and coordinate files (.gro) and generated 
parameter (.itp) file using following command (Thanks to Tsjerk):
sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e 
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP


But the topology and co-ordinates file are quite different from the 
input PDB file and hence the parameters are also faulty, the GDP 
molecule is not fitting in the binding pocket of protein. Upon 
tracking the whole process, it was found that the error might be while 
using antechamber for generating prepin file using Gaussian output 
file as the input.


Can anyone please suggest some way to apply some constraints in the 
antechamber command itself. OR if anybody has the paramters or 
topology for GDP, can anyone provide me the same so that I can compare 
and see where the parameters are differing.


Surely antechamber will accept whatever coordinate file you provide to 
it, and the AMBER mailing list is the place to make inquiries about it 
(after checking the documentation).


Don't stress too much about the charges - those that are suitable in the 
bound and unbound form will normally be different, and current methods 
can't access the former.


Mark
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Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

2011-12-09 Thread Matthew Zwier 
Hi Ruhollah,

A while ago on the list there was a discussion of extreme memory use
and possibly-incorrect results from g_msd under some conditions.  The
problem could be worked around by imaging the trajectory with trjconv
first to remove jumps across the box, then running g_msd on the
results.  Perhaps you'll have some more success with that workflow.

Cheers,
Matt Z.

On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi
 wrote:
> David,
> thank you for your reply.
>
> but, g_msd gives a diffusion coefficient which is one order of magnitude
> higher than expected for a small polypeptide (15 res long with gyration Rg ~
> 0.8nm) with the same size. this is command line i used:
> g_msd-mpi -f  md_mine_2nd.xtc -s  md_mine_2nd.tpr -o  msd_2nd.xvg
>
> when visualizing, I can see that the polypeptide crosses the boundary
> several times. apparently,  g_msd counts these 'artificial' jumps in MSD
> calculation.  and, that's probably why the diffusion coefficient is
> calculated such high (i.e. 500 um2/s for a small protein).
>
> if this is the case, it is a bug in g_msd I believe.
>
> is there any way to get round this problem?
>
> -- Forwarded message --
> From: Anonymous 
> Date: Fri, Dec 9, 2011 at 12:17 AM
> Subject: Comment for Forum topic: diffusion coefficient
> To: ruhollah...@gmail.com
>
>
> Hi ruhollahmoussavi-baygi,
>
> Comment by davidvanderspoel: diffusion coefficient
>
>
> On 2011-12-09 08:34, Mark Abraham wrote:
>> On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
>>> I want to calculate the diffusion coefficient of a small polypeptide
>>> with g_msd (see here
>>> http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [1])
>>>
>>> because of periodic boundary condition, when the peptide goes out of
>>> the right side it comes in from left side, which leads to an
>>> artificial displacement. this will give rise to a non-realistic MSD.
>>>
>>> is g_msd intelligent enough to avoid this artificial displacement?
>>>
>>
> Yes it is.
>
>
>> Not sure about g_msd, but you can take care of it yourself with a
>> workflow derived from the information here
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi...
>> [2]
>>
>>
>> Mark
>
> Read more
> http://support.scalalife.eu/content/diffusion-coefficient#comment-103
>
>
> --
>
> This is an automatic message from ScalaLife To manage your subscriptions,
> browse to http://support.scalalife.eu/user/291/notifications You can
> unsubscribe at
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>
>
> [1] http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant
> [2]
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
>
>
> --
> Best,
> Ruhollah Moussavi-Baygi
>
> --
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Re: [gmx-users] mdrun_mpi error

2011-12-09 Thread aiswarya pawar 
Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d
-qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450"

and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
libmd_mpi.la'.  Stop.
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the
future
/bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
-qtune=450 -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
/home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1


On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham wrote:

> On 8/12/2011 6:35 PM, aiswarya pawar wrote:
>
>> Hi users,
>>
>> Am running the mdrun_mpi on cluster with the md.mdp parameters as-
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> title= Position Restrained Molecular Dynamics
>>
>>
>> ; RUN CONTROL PARAMETERS
>> constraints = all-bonds
>> integrator = md
>> dt = 0.002 ; 2fs !
>> nsteps = 250 ; total 5000 ps.
>> nstcomm = 10
>> nstxout = 500 ; collect data every 1 ps
>> nstxtcout = 500
>> nstvout = 0
>> nstfout = 0
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdwtype = cut-off
>> rvdw = 1.4
>> pme_order = 4
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> DispCorr = no
>> ; Berendsen temperature coupling is on
>> Tcoupl = v-rescale
>> tau_t = 0.1 0.1
>> tc-grps = protein non-protein
>> ref_t = 300 300
>> ; Pressure coupling is on
>> Pcoupl = parrinello-rahman
>> Pcoupltype = isotropic
>> tau_p = 1.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = -1
>>
>>
>> The grompp runs fine. but when i run the mdrun_mpi i get an error such as-
>>
>> Child exited abnormally!
>> Killing remote processes...DONE
>>
>
> There's no information here upon which one can diagnose anything. Look at
> the stderr, stdout and .log files and consult the errors page on the
> GROMACS website for clues.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] mdrun_mpi error

2011-12-09 Thread aiswarya pawar 
Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d
-qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450"

and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/
gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
libmd_mpi.la'.  Stop.
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the
future
/bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
-qtune=450 -no-undefined -version-info 6:0:0  -L/home/soft/lib  -o
libgmxpreprocess_mpi.la -rpath /home/soft/gromacs/lib add_par.lo
compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo
gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo
pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo
ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo
toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl
-lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1

On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar wrote:

> Hi,
>
> I tried giving this-
>
>
> ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
> --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d
> -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450"
>
> and the configure process ran well.
>
> but when i gave make mdrun, i get an error which says=
>
> make[2]: *** [vmdio.lo] Error 1
> make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
> (cd ./src/mdlib && make ; exit 0)
> make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
> make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
> future
> make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
> libmd_mpi.la'.  Stop.
> make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
> (cd ./src/kernel && make mdrun ; exit 0)
> make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
> make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the
> future
> /bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
> -qtune=450 -no-undefined -version-info 6:0:0
> -L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
> /home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
> convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
> gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
> readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
> topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
> vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
> unhandled argument `../mdlib/libmd_mpi.la'
> make[1]: *** [libgmxpreprocess_mpi.la] Error 1
>
>
>
> On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham wrote:
>
>> On 8/12/2011 6:35 PM, aiswarya pawar wrote:
>>
>>> Hi users,
>>>
>>> Am running the mdrun_mpi on cluster with the md.mdp parameters as-
>>>
>>> ; VARIOUS PREPROCESSING OPTIONS
>>> title= Position Restrained Molecular Dynamics
>>>
>>>
>>> ; RUN CONTROL PARAMETERS
>>> constraints = all-bonds
>>> integrator = md
>>> dt = 0.002 ; 2fs !
>>> nsteps = 250 ; total 5000 ps.
>>> nstcomm = 10
>>> nstxout = 500 ; collect data every 1 ps
>>> nstxtcout = 500
>>> nstvout = 0
>>> nstfout = 0
>>> nstlist = 10
>>> ns_type = grid
>>> rlist = 1.0
>>> coulombtype = PME
>>> rcoulomb = 1.0
>>> vdwtype = cut-off
>>> rvdw = 1.4
>>> pme_order = 4
>>> ewald_rtol = 1e-5
>>> optimize_fft = yes
>>> DispCorr = no
>>> ; Berendsen temperature coupling is on
>>> Tcoupl = v-rescale
>>> tau_t = 0.1 0.1
>>> tc-grps = protein non-protein
>>> ref_t = 300 300
>>> ; Pressure coupling is on
>>> Pcoupl = parrinello-rahman
>>> Pcoupltype = isotropic
>>> tau_p = 1.0
>>> compressibility = 4.5e-5
>>> ref_p = 1.0
>>> ; Generate velocites is on at 300 K.
>>> gen_vel = yes
>>> gen_temp = 300.0
>>> gen_seed = -1
>>>
>>>
>>> The grompp runs fine. but when i run the mdrun_mpi i get an error such
>>> as-
>>>
>>> Child exited abnorm

Re: [gmx-users] mdrun_mpi error

2011-12-09 Thread Mark Abraham 

On 10/12/2011 6:31 PM, aiswarya pawar wrote:


Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 
--enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 
-qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d 
-qtune=450"


and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1


The first error happened above this line, so we can't tell what is 
wrong. As a wild guess, use --without-dlopen with configure.


Mark


make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/
gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in 
the future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la 
', needed by `libmd_mpi.la 
'.  Stop.

make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in 
the future
/bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d 
-qtune=450 -no-undefined -version-info 6:0:0  -L/home/soft/lib  -o 
libgmxpreprocess_mpi.la  -rpath 
/home/soft/gromacs/lib add_par.lo compute_io.lo convparm.lo 
fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo 
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo 
pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo 
ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo 
topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo 
../mdlib/libmd_mpi.la  -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la 
' or unhandled argument `../mdlib/libmd_mpi.la 
'
make[1]: *** [libgmxpreprocess_mpi.la 
] Error 1


On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar 
mailto:aiswarya.pa...@gmail.com>> wrote:


Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3
-qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d
-qtune=450"

and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 7.6e+02 s
in the future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la
', needed by `libmd_mpi.la
'.  Stop.
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 7.5e+02 s
in the future
/bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
-qtune=450 -no-undefined -version-info 6:0:0 
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la

 -rpath
/home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo
gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo
hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo
sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo
topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo
xlate.lo ../mdlib/libmd_mpi.la  -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la
' or unhandled argument
`../mdlib/libmd_mpi.la '
make[1]: *** [libgmxpreprocess_mpi.la
] Error 1



On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 8/12/2011 6:35 PM, aiswarya pawar wrote:

Hi users,

Am running the mdrun_mpi on cluster with the md.mdp
parameters as-

; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular
Dynamics


; RUN CONTROL PARAMETERS
constraints = all-bonds
integrator = md
dt = 0.002 ; 2fs !
nsteps = 250 ; total 5000 ps.
ns