[gmx-users] RE: Diffusion coefficients ( Exp X Simul )

[Vitaly V. Chaban]

>Hello, someone could suggest me references
>which discusses the difficulty of obtaining
>values for diffusion coefficients in agreement
>to the experimental values? For water that
>is well known, but I do not know of any
>reference that discusses this topic
>Thanks

Hi,

There's a bunch of papers discussing diffusion constants
reproducibility. Just look for ones describing the force field models
you use. Experimental diffusion constants are often listed there.

Vitaly

-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
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Re: [gmx-users] combination rules -- the part aboutthecombinationrules

[Mark Abraham]

Shuangxing Dai wrote:
Thank you for your help. I checked all the force field, all of them are 
with default non-bond params in LJ. So I still need to try new solution.
I add my non bond parameters in the .top file generated. Force field 
files were not changed. Then I use grompp, the error was:


That wasn't the question. Do you *need* the rest of the force field? If 
you're only doing ZnO then you don't need the rest. IIRC you've never 
told us what you're trying to simulate, which tends to frustrate any 
effort to help you.



'[ nonbond_params ]'

Invalid order for directive nonbond_params


Yep, these can't appear anywhere after a [molecule] directive. See 
chapter 5 of the manual.



Rather confused by setting up Buckingham potential parameters...


Make sure you read the advice you're being given:


If you need other atoms as well, you will need to find
a consistent force field, probably or completely LJ
or completely Buckingham.


and


 > No, because it's not a reasonable goal. Your new atomtypes are
talking a
 > different vdW "language". That doesn't work.


and

 > > And what
 > > force field to choose if not ffgmx?
 >
 > That's your homework I'm afraid. You'll have to read the literature.


Cheers,

Mark
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Re: [gmx-users] combination rules -- the part aboutthecombinationrules

[Shuangxing Dai]

Thank you for your help. I checked all the force field, all of them are with
default non-bond params in LJ. So I still need to try new solution.
I add my non bond parameters in the .top file generated. Force field files
were not changed. Then I use grompp, the error was:


'[ nonbond_params ]'

Invalid order for directive nonbond_params
Rather confused by setting up Buckingham potential parameters...
Thank you very much!

2009/2/26 Berk Hess 

> Hi,
>
> But do you need any other parameters than zinc and oxide?
> If not, you can simply remove all other parameters.
> If you need other atoms as well, you will need to find
> a consistent force field, probably or completely LJ
> or completely Buckingham.
>
> Berk
>
> > Date: Thu, 26 Feb 2009 09:22:26 +1100
> > From: mark.abra...@anu.edu.au
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] combination rules -- the part
> aboutthecombinationrules
> >
>  > Shuangxing Dai wrote:
> > > Yes, "add parameters for crystalline zinc oxide, which require
> > > Buckingham nonbonded interactions", that is what I am doing. I think I
> > > have changed all the necessary parts for the Buckingham potential. Is
> > > there any direct way to accomplish my goal?
> >
> > No, because it's not a reasonable goal. Your new atomtypes are talking a
> > different vdW "language". That doesn't work.
> >
> > > Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type
>
> > > is 1. I only changed the parameters for Zn and O to Buckingham
> > > parameters. And you said "add your functions in the right form in your
> [
> > > molecule ] section" , I cannot find the right place to change.
> >
> > Chapter 5 of the manual.
> >
> > > And what
> > > force field to choose if not ffgmx?
> >
> > That's your homework I'm afraid. You'll have to read the literature.
> >
> > Mark
> > ___
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-- 
Shuangxing Dai
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Re: [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

[Mark Abraham]

chris.ne...@utoronto.ca wrote:

Thanks Mark,

your information is always useful. In this case, the page that you 
reference appears to be empty. All I see is "There is currently no text 
in this page, you can search for this page title in other pages or edit 
this page."


Thanks also for your consideration of the massive scaling issue.


The link works fine for me. Try the one from 
http://wiki.gromacs.org/index.php/Installation#Specialty_Instructions to 
that URL.


In any case, one line to which I was referring was

./configure LDFLAGS="-lnss_files -lnss_dns -lresolv -lc -lnss_files 
-lnss_dns -lresolv"


Mark
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[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

[chris . neale]

Thanks Roland,

The system has 500,000 atoms. I use PME and a 0.9 nm cutoff for  
coulombic and a 1.4/0.9 nm twin range cutoff for LJ. The interconnect  
is infiniband between power6 nodes that each have 32 cores @ 4.2 GHz  
that are multithreaded so that I can put 64 "tasks" on each  
node. The scaling on the power6 is like this:


N=1    0.036 ns/day  (Scaling Efficiency)
N=2    0.070 ns/day  (97%)
N=4    0.135 ns/day  (94%)
N=8    0.246 ns/day  (85%)
N=16   0.449 ns/day  (75%)
N=32   0.787 ns/day  (68%)
N=60   0.984 ns/day  (46%)
And I have errors above N=60.

In terms of what you want from the log file, are you referring to  
general scaling issues for, for example, N=32, which does run  
successfully? Or are you rather requesting more log file information  
to assist me deal with my errors while running 196 or 200  
"tasks"?


Thanks so much for your help Roland,
Chris.

-- original message --

Chris,

depending on your system size and th interconnect this might be OK.

Thus you need to give us more information. E.g.: how many atoms, how  
many

ns/day, what interconnect, PME?.

Also the messages at the end of the md.log might tell you some advices  
to

improve performance.

Roland

On Tue, Mar 3, 2009 at 10:48 PM,  wrote:

[Hide Quoted Text]
Thanks Mark,

your information is always useful. In this case, the page that you
reference appears to be empty. All I see is "There is currently  
no text in
this page, you can search for this page title in other pages or edit  
this

page."

Thanks also for your consideration of the massive scaling issue.

Chris.

chris.neale at utoronto.ca wrote:
Hello,

I am currently testing a large system on a power6 cluster. I have  
compiled

gromacs 4.0.4 successfully, and it appears to be working fine for <64
"cores" (sic, see later). First, I notice that it runs at  
approximately 1/2
the speed that it obtains on some older opterons, which is unfortunate  
but

acceptable. Second, I run into some strange issues when I have a greater
number of cores. Since there are 32 cores per node with simultaneous
multithreading this yields 64 tasks inside one box, and I realize that  
these

problems could be MPI related.

Some background:
This test system is stable for > 100ns on an opteron so I am quite
confident that I do not have a problem with my topology or starting
structure.

Compilation was successful with -O2 only when I modified the ./configure
file as follows, otherwise I got a stray ')' and a linking error:
[cneale at tcs-f11n05]$ diff configure.000 configure
5052a5053
ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib  
-lxlf90

-L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm -lc"
Rather than modify configure, I suggest you use a customized command  
line, such as the one described here
href="http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene";>http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output/>

config.log will have a record of what you did, too.

Sorry I can't help with the massive scaling issue.

Mark

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Re: [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

[Roland Schulz]

Chris,

depending on your system size and th interconnect this might be OK.

Thus you need to give us more information. E.g.: how many atoms, how many
ns/day, what interconnect, PME?.

Also the messages at the end of the md.log might tell you some advices to
improve performance.

Roland

On Tue, Mar 3, 2009 at 10:48 PM,  wrote:

> Thanks Mark,
>
> your information is always useful. In this case, the page that you
> reference appears to be empty. All I see is "There is currently no text in
> this page, you can search for this page title in other pages or edit this
> page."
>
> Thanks also for your consideration of the massive scaling issue.
>
> Chris.
>
> chris.neale at utoronto.ca wrote:
>
>> Hello,
>>
>> I am currently testing a large system on a power6 cluster. I have compiled
>> gromacs 4.0.4 successfully, and it appears to be working fine for <64
>> "cores" (sic, see later). First, I notice that it runs at approximately 1/2
>> the speed that it obtains on some older opterons, which is unfortunate but
>> acceptable. Second, I run into some strange issues when I have a greater
>> number of cores. Since there are 32 cores per node with simultaneous
>> multithreading this yields 64 tasks inside one box, and I realize that these
>> problems could be MPI related.
>>
>> Some background:
>> This test system is stable for > 100ns on an opteron so I am quite
>> confident that I do not have a problem with my topology or starting
>> structure.
>>
>> Compilation was successful with -O2 only when I modified the ./configure
>> file as follows, otherwise I got a stray ')' and a linking error:
>> [cneale at tcs-f11n05]$ diff configure.000 configure
>> 5052a5053
>>
>>> ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib -lxlf90
>>> -L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm -lc"
>>>
>>
> Rather than modify configure, I suggest you use a customized command
> line, such as the one described here
> http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output
> config.log will have a record of what you did, too.
>
> Sorry I can't help with the massive scaling issue.
>
> Mark
>
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-- 
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865-241-1537, ORNL PO BOX 2008 MS6309
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[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

[chris . neale]

Thanks Mark,

your information is always useful. In this case, the page that you  
reference appears to be empty. All I see is "There is currently no  
text in this page, you can search for this page title in other pages  
or edit this page."


Thanks also for your consideration of the massive scaling issue.

Chris.

chris.neale at utoronto.ca wrote:

Hello,

I am currently testing a large system on a power6 cluster. I have  
compiled gromacs 4.0.4 successfully, and it appears to be working  
fine for <64 "cores" (sic, see later). First, I notice that it runs  
at approximately 1/2 the speed that it obtains on some older  
opterons, which is unfortunate but acceptable. Second, I run into  
some strange issues when I have a greater number of cores. Since  
there are 32 cores per node with simultaneous multithreading this  
yields 64 tasks inside one box, and I realize that these problems  
could be MPI related.


Some background:
This test system is stable for > 100ns on an opteron so I am quite  
confident that I do not have a problem with my topology or starting  
structure.


Compilation was successful with -O2 only when I modified the  
./configure file as follows, otherwise I got a stray ')' and a  
linking error:

[cneale at tcs-f11n05]$ diff configure.000 configure
5052a5053
ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib  
-lxlf90 -L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm  
-lc"


Rather than modify configure, I suggest you use a customized command
line, such as the one described here
http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output
config.log will have a record of what you did, too.

Sorry I can't help with the massive scaling issue.

Mark

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Re: [gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

[Mark Abraham]

chris.ne...@utoronto.ca wrote:

Hello,

I am currently testing a large system on a power6 cluster. I have 
compiled gromacs 4.0.4 successfully, and it appears to be working fine 
for <64 "cores" (sic, see later). First, I notice that it runs at 
approximately 1/2 the speed that it obtains on some older opterons, 
which is unfortunate but acceptable. Second, I run into some strange 
issues when I have a greater number of cores. Since there are 32 cores 
per node with simultaneous multithreading this yields 64 tasks inside 
one box, and I realize that these problems could be MPI related.


Some background:
This test system is stable for > 100ns on an opteron so I am quite 
confident that I do not have a problem with my topology or starting 
structure.


Compilation was successful with -O2 only when I modified the ./configure 
file as follows, otherwise I got a stray ')' and a linking error:

[cne...@tcs-f11n05]$ diff configure.000 configure
5052a5053
ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib -lxlf90 
-L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm -lc"


Rather than modify configure, I suggest you use a customized command 
line, such as the one described here 
http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output 
config.log will have a record of what you did, too.


Sorry I can't help with the massive scaling issue.

Mark
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Re: [gmx-users] g_wham 4..0.x input file: tpr-files.dat ?

[Justin A. Lemkul]

Y.C. Huang wrote:

Hello everyone:

I have a question about the g_wham version 4.0.x.
After I tried to do umbrella sampling by using mdrun 4.0.x, I had these
files:

pullf.xvg pullx.xvg umbrella_test.err umbrella_test.tpr umbrella_test.gro
umbrella_test.trr umbrella_test.edr umbrella_test.log umbrella_test_prev.cpt
umbrella_test.cpt

In order to get the energy profile, I use this command

g_wham -ix pullx.xvg -it umbrella_test.tpr -o profile.xvg -hist histo.xvg
or
g_wham -if pullf.xvg -it umbrella_test.tpr -o profile.xvg -hist histo.xvg


But I saw the error message:

File input/output error:
umbrella_test.tpr.dat

Did I missing something? Please help me.



Read g_wham -h for the file types needed as input.

-Justin










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--


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


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[gmx-users] g_wham 4..0.x input file: tpr-files.dat ?

[Y.C. Huang]

Hello everyone:

I have a question about the g_wham version 4.0.x.
After I tried to do umbrella sampling by using mdrun 4.0.x, I had these
files:

pullf.xvg pullx.xvg umbrella_test.err umbrella_test.tpr umbrella_test.gro
umbrella_test.trr umbrella_test.edr umbrella_test.log umbrella_test_prev.cpt
umbrella_test.cpt

In order to get the energy profile, I use this command

g_wham -ix pullx.xvg -it umbrella_test.tpr -o profile.xvg -hist histo.xvg
or
g_wham -if pullf.xvg -it umbrella_test.tpr -o profile.xvg -hist histo.xvg


But I saw the error message:

File input/output error:
umbrella_test.tpr.dat

Did I missing something? Please help me.









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[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

[chris . neale]

Hello,

I am currently testing a large system on a power6 cluster. I have  
compiled gromacs 4.0.4 successfully, and it appears to be working fine  
for <64 "cores" (sic, see later). First, I notice that it runs at  
approximately 1/2 the speed that it obtains on some older opterons,  
which is unfortunate but acceptable. Second, I run into some strange  
issues when I have a greater number of cores. Since there are 32 cores  
per node with simultaneous multithreading this yields 64 tasks inside  
one box, and I realize that these problems could be MPI related.


Some background:
This test system is stable for > 100ns on an opteron so I am quite  
confident that I do not have a problem with my topology or starting  
structure.


Compilation was successful with -O2 only when I modified the  
./configure file as follows, otherwise I got a stray ')' and a linking  
error:

[cne...@tcs-f11n05]$ diff configure.000 configure
5052a5053
ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib  
-lxlf90 -L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm  
-lc"


The error messages:
For N=1,2,4,8,16,32, and 64, the system runs properly.
For N=200, I get the error: "ERROR: 0032-103 Invalid count  (-8388608)  
in MPI_Recv, task 37"
For N=196 my system explodes via regular settle/lings warnings  
followed by a crash.


Here are the log file and stderr snippits

On 200 cores:

The log file appears normal but is truncated.

## stderr:
...
Will use 112 particle-particle and 88 PME only nodes
This is a guess, check the performance at the end of the log file

NOTE: For optimal PME load balancing at high parallelization
  PME grid_x (175) and grid_y (175) should be divisible by #PME_nodes (88)

Making 3D domain decomposition 4 x 7 x 4

starting mdrun 'Big Box'
500 steps,  1.0 ps.
ERROR: 0032-103 Invalid count  (-8388608) in MPI_Recv, task 37


#

On 196 cores,

...
Initializing Domain Decomposition on 196 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.556 nm, LJ-14, atoms 25035 25038
  multi-body bonded interactions: 0.556 nm, Proper Dih., atoms 25035 25038
Minimum cell size due to bonded interactions: 0.612 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nm
Estimated maximum distance required for P-LINCS: 0.820 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.37
Will use 108 particle-particle and 88 PME only nodes
This is a guess, check the performance at the end of the log file
Using 88 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 108 cells with a minimum initial size of 1.025 nm
The maximum allowed number of cells is: X 16 Y 16 Z 14
Domain decomposition grid 6 x 6 x 3, separate PME nodes 88
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 4 groups of on average 27.0 processes
...


# And to stderr, I get:
...
Back Off! I just backed up temp.log to ./#temp.log.2#
Reading file temp.tpr, VERSION 4.0.4 (single precision)

Will use 108 particle-particle and 88 PME only nodes
This is a guess, check the performance at the end of the log file

NOTE: For optimal PME load balancing at high parallelization
  PME grid_x (175) and grid_y (175) should be divisible by #PME_nodes (88)

Making 3D domain decomposition 6 x 6 x 3

starting mdrun 'Big Box'
500 steps,  1.0 ps.

Step 61, time 0.122 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002765, max 0.028338 (between atoms 46146 and 46145)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  46148  46146   89.90.1480   0.1499  0.1480
  46050  46049   32.00.1470   0.1475  0.1470

t = 0.122 ps: Water molecule starting at atom 62389 can not be settled.
Check for bad contacts and/or reduce the timestep.

t = 0.122 ps: Water molecule starting at atom 706505 can not be settled.

...

### And the system then proceeds to explode.

###

I am happy to provide more information, and apologize if what I have  
posted here is incomplete. These log files are large though, and I  
tried to keep this first post as short as possible.


Thanks for any assistance,
Chris.

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Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

[David van der Spoel]

Eudes Fileti wrote:
Hello, someone could suggest me references 
which discusses the difficulty of obtaining 
values for diffusion coefficients in agreement 
to the experimental values? For water that 
is well known, but I do not know of any 
reference that discusses this topic


You mean that models do not reproduce D?
You could have a look at JCP 119 pp. 7308-7317 (2003) and references 
therein. There is quite a lot of literature.



Thanks
eef
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+55.11.4437-8408
skype: eefileti
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] Diffusion coefficients ( Exp X Simul )

[Eudes Fileti]

Hello, someone could suggest me references
which discusses the difficulty of obtaining
values for diffusion coefficients in agreement
to the experimental values? For water that
is well known, but I do not know of any
reference that discusses this topic
Thanks
eef
___
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Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
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Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

On Wed, Mar 4, 2009 at 2:25 AM, Mark Abraham wrote:

> Manik Mayur wrote:
>
>>
>>
>> On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz > rol...@utk.edu>> wrote:
>>
>>You will have to recompile everything:
>>make clean
>>make
>>
>>
>> I tried that but to no avail, then I tried building static libs by
>> removing --enable-shared in ./configure and it got compiled and installed
>> properly.
>> Thanks to all, as for now, its working to my need.
>> But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon
>> Quad core at 3.6Ghz, the processing speed which I am getting, is quite low.
>>
>
> This comment won't help you fix the issue. You need to start by telling us
> why you think the speed is low, and under what conditions you are testing.
> If you aren't using an optimized FFT package you will get slow throughput
> with PME.


Yes, I do need to run some more tests before commenting on the speed issue.
However, I just found that the processor is not Xeon Quad core @ 3.6 Ghz.
The output of $cat /proc/cpuinfo is:

-bash-2.05b$ cat /proc/cpuinfo
processor: 0
vendor_id: GenuineIntel
cpu family: 15
model: 4
model name: Intel(R) Xeon(TM) CPU 3.60GHz
stepping: 1
cpu MHz: 3600.248
cache size: 1024 KB
physical id: 0
siblings: 2
runqueue: 0
fdiv_bug: no
hlt_bug: no
f00f_bug: no
coma_bug: no
fpu: yes
fpu_exception: yes
cpuid level: 5
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm nx lm
bogomips: 7182.74

processor: 1
vendor_id: GenuineIntel
cpu family: 15
model: 4
model name: Intel(R) Xeon(TM) CPU 3.60GHz
stepping: 1
cpu MHz: 3600.248
cache size: 1024 KB
physical id: 3
siblings: 2
runqueue: 1
fdiv_bug: no
hlt_bug: no
f00f_bug: no
coma_bug: no
fpu: yes
fpu_exception: yes
cpuid level: 5
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm nx lm
bogomips: 7182.74

processor: 2
vendor_id: GenuineIntel
cpu family: 15
model: 4
model name: Intel(R) Xeon(TM) CPU 3.60GHz
stepping: 1
cpu MHz: 3600.248
cache size: 1024 KB
physical id: 0
siblings: 2
runqueue: 0
fdiv_bug: no
hlt_bug: no
f00f_bug: no
coma_bug: no
fpu: yes
fpu_exception: yes
cpuid level: 5
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm nx lm
bogomips: 7182.74

processor: 3
vendor_id: GenuineIntel
cpu family: 15
model: 4
model name: Intel(R) Xeon(TM) CPU 3.60GHz
stepping: 1
cpu MHz: 3600.248
cache size: 1024 KB
physical id: 3
siblings: 2
runqueue: 1
fdiv_bug: no
hlt_bug: no
f00f_bug: no
coma_bug: no
fpu: yes
fpu_exception: yes
cpuid level: 5
wp: yes
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm nx lm
bogomips: 7182.74

Mark
>
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Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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Re: [gmx-users] gromacs on itanium2

[Erik Lindahl]

Hi,

There have been some reports on newer ia64 processors being quite fast  
with the Fortran kernels instead (even faster than asm!), so I would  
try that.


This has to do with the brain-dead architecture on ia64. The asm  
kernels were written for original itanium2 timings, but with the  
register rotation loops and lack of dynamic instruction scheduling you  
would get lots of pipeline stalls/bubbles if Intel ever changed their  
instruction latencies, and that might have happend now.


Considering the limited adoption of ia64 I don't think we're very  
likely to keep updating those kernels - the first thing on the agenda  
right now will rather be improved performance of x86 SSE kernels for  
Gromacs 4.1.


Cheers,

Erik


On Mar 3, 2009, at 8:14 PM, David van der Spoel wrote:


Marius Retegan wrote:

Hello
Since I was unable to get a working version for Gromacs 4.0.4 on a
Itanium 2 machine with the ia64 nonbonded kernel, I was wondering  
what

would be the lost in speed if I would disable the assembly loops?

About a factor of two. What's the problem with compiling?


Thanks,
Marius
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
University.

Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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Re: [gmx-users] Problem configuring openMPI

[Mark Abraham]

Manik Mayur wrote:



On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz > wrote:


You will have to recompile everything:
make clean
make


I tried that but to no avail, then I tried building static libs by 
removing --enable-shared in ./configure and it got compiled and 
installed properly.

Thanks to all, as for now, its working to my need.
But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon 
Quad core at 3.6Ghz, the processing speed which I am getting, is quite low.


This comment won't help you fix the issue. You need to start by telling 
us why you think the speed is low, and under what conditions you are 
testing. If you aren't using an optimized FFT package you will get slow 
throughput with PME.


Mark
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Re: [gmx-users] (no subject)

[Mark Abraham]

Antonia Vyrkou wrote:

Hello,

I am trying to simulate a system for which I need to exclude all
intramolecular culombic interactions except those included in the pair_list. 
How can I do that?


Perhaps by use of energy group exclusions - see the manual.


Also, the pairs defined at the [ pairs ] section are used for both
Lennard-Jones and coulombic interaction, are they not?


I think so.

Mark
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Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz  wrote:

> You will have to recompile everything:
> make clean
> make
>

I tried that but to no avail, then I tried building static libs by removing
--enable-shared in ./configure and it got compiled and installed properly.
Thanks to all, as for now, its working to my need.
But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon Quad
core at 3.6Ghz, the processing speed which I am getting, is quite low.

You still have references to lam in your libmd_mpi.so
>
> Roland
>
> On Tue, Mar 3, 2009 at 3:03 PM, Manik Mayur  wrote:
>
>>
>>
>> On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz  wrote:
>>
>>> you will have to set
>>>
>>> LD_LIBRARY_PATH to /home/openmpi/lib
>>>
>>
>> I have tried that.. the error still persists.
>> - Show quoted text -
>>
>>
>> use either setenv or export depending on your shell
>>>
>>> Roland
>>>
>>> On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur wrote:
>>>
 this time upon executing :
 ./configure\
--prefix /home/local/gromacs\
--enable-mpi\
--program-suffix="_mpi"\
--disable-nice\
--enable-shared\
MPICC=/home/openmpi/mpicc\

 it exited with the following error:

 ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `rw'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to
 `lam_deregister_object'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to
 `lam_register_objects'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to
 `sfh_sock_accept_tmout'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to
 `sfh_sock_open_srv_inet_stm'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to
 `sfh_sock_set_buf_size'
 ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand'
 ../mdlib/.libs/libmd_mpi.so: undefined 

Re: [gmx-users] gromacs on itanium2

[Mark Abraham]

Marius Retegan wrote:

Hi,
First I've managed to compile 3.3.1 with Intel 9.1 and assembly loops
for ia64. Then I've tried 3.3.3 and 4.0.4. For both I've got a similar
error:

/bin/sh ../../../../libtool   --mode=compile icc -DHAVE_CONFIG_H -I.
-I../../../../src -I/usr/X11R6/include -I../../../../include
-DGMXLIBDIR=\"/fougeron/home/mretegan/software/gromacs-4.0.4/share/top\"
-I/fougeron/home/mretegan/software/fftw3/include  -O2 -mtune=itanium2
-MT nb_kernel010_ia64_single.lo -MD -MP -MF
.deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo
nb_kernel010_ia64_single.S
 icc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include
-I../../../../include
-DGMXLIBDIR=\"/fougeron/home/mretegan/software/gromacs-4.0.4/share/top\"
-I/fougeron/home/mretegan/software/fftw3/include -O2 -mtune=itanium2
-MT nb_kernel010_ia64_single.lo -MD -MP -MF
.deps/nb_kernel010_ia64_single.Tpo -c nb_kernel010_ia64_single.S -o
nb_kernel010_ia64_single.o
/tmp/iccDePOHl.s(1) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(2) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(3) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(4) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(5) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(6) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(7) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(8) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(10) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(15) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(193) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(195) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(269) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(423) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(506) : error A2040: Unexpected token: Unary Diez
Operator at: Start
nb_kernel010_ia64_single.o - 15 error(s), 0 warning(s)


After I started looking on the archive and I've found the this thread
http://www.mail-archive.com/gmx-users@gromacs.org/msg16911.html. Then
I've installed the latest Intel compilers (11.0) and I've managed to
get it compiled. Unfortunately when I've tested the build, the complex
test failed without producing any output (not even test FAILED). I
tried to run them by hand, but strangely after I ran the mdrun command
they just kept on running. No error whatsoever.

The fftw were compiled with the same compiler as Gromacs. I've use O2
optimizations in CFLAGS.


There's been another thread this year (I think) and a bugzilla filed on 
this topic. In the meantime, it's quite reasonable to use configure 
--enable-fortran for IA64, as Berk(?) suggested in that thread.


Mark


On Tue, Mar 3, 2009 at 8:14 PM, David van der Spoel
 wrote:

Marius Retegan wrote:

Hello

Since I was unable to get a working version for Gromacs 4.0.4 on a
Itanium 2 machine with the ia64 nonbonded kernel, I was wondering what
would be the lost in speed if I would disable the assembly loops?


About a factor of two. What's the problem with compiling?


Thanks,
Marius
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Re: [gmx-users] Can not open file: topol.tpr

[Mark Abraham]

drugdesign wrote:

Oh, I am very sorry, I've copied the wrong error.


That's life - but one needs to be methodical and exacting with science 
in general and computational chemistry in particular.



Actually error was with the same tutorial at the next step with mdrun -v deffnm 
em.
I can't figure  out why I need topol.tpr for energy minimization? It must be 
only em.tpr, right? by -v deffnm command?

---
Program mdrun, VERSION 4.0.2
Source code file: gmxfio.c, line: 736

Can not open file:
topol.tpr
---


Well, at least you copied and pasted your mdrun command line correctly, 
but you didn't form it correctly in the first place. It needs to be


mdrun -v -deffnm em

There are default file names for all files supplied by options to 
GROMACS programs. If GROMACS can't interpret the information you supply, 
you might get such an error when it also can't find the default 
necessary filenames.


Mark
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Re: [gmx-users] How to define protein surface residues

[Mark Abraham]

Lee Soin wrote:
Thanks, but what I mean is to just find out the surface residues, not to 
calculate the surface area.


So use g_sas to plot the area per residue and look at the ones for which 
it is non-zero.


Mark

2009/3/3 David van der Spoel >


Lee Soin wrote:

Hello!
I'm trying to find the surface residues of a protein. Maybe this
should be calculated by myself and not using GROMACS. Can
anybody tell me a feasible procedure for doing so? Thanks!

g_sas

-- 
Sun Li

Department of Physics
Nanjing University, China




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-- 
David van der Spoel, Ph.D., Professor of Biology

Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se   
 sp...@gromacs.org   
http://folding.bmc.uu.se 

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Re: [gmx-users] Problem configuring openMPI

[Roland Schulz]

You will have to recompile everything:
make clean
make

You still have references to lam in your libmd_mpi.so

Roland

On Tue, Mar 3, 2009 at 3:03 PM, Manik Mayur  wrote:

>
>
> On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz  wrote:
>
>> you will have to set
>>
>> LD_LIBRARY_PATH to /home/openmpi/lib
>>
>
> I have tried that.. the error still persists.- Show quoted text -
>
>
> use either setenv or export depending on your shell
>>
>> Roland
>>
>> On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur wrote:
>>
>>> this time upon executing :
>>> ./configure\
>>>--prefix /home/local/gromacs\
>>>--enable-mpi\
>>>--program-suffix="_mpi"\
>>>--disable-nice\
>>>--enable-shared\
>>>MPICC=/home/openmpi/mpicc\
>>>
>>> it exited with the following error:
>>>
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rw'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>>> `lam_deregister_object'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>>> `lam_register_objects'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>>> `sfh_sock_accept_tmout'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>>> `sfh_sock_open_srv_inet_stm'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>>> `sfh_sock_set_buf_size'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_find'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getorigin'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamesweep'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_lam_signal'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>>> `sfh_sock_open_clt_inet_stm'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpstate'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `tprintf'
>>> ../mdlib/.libs/libmd_mpi.so: undefined reference to

Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz  wrote:

> you will have to set
>
> LD_LIBRARY_PATH to /home/openmpi/lib
>

I have tried that.. the error still persists.

use either setenv or export depending on your shell
>
> Roland
>
> On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur  wrote:
>
>> this time upon executing :
>> ./configure\
>>--prefix /home/local/gromacs\
>>--enable-mpi\
>>--program-suffix="_mpi"\
>>--disable-nice\
>>--enable-shared\
>>MPICC=/home/openmpi/mpicc\
>>
>> it exited with the following error:
>>
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rw'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>> `lam_deregister_object'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_register_objects'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>> `sfh_sock_accept_tmout'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>> `sfh_sock_open_srv_inet_stm'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>> `sfh_sock_set_buf_size'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_find'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getorigin'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamesweep'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_lam_signal'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to
>> `sfh_sock_open_clt_inet_stm'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpstate'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `tprintf'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kpause'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_next'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rev8'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvadd'
>> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiselect'
>> ../mdlib/.libs/libmd_mpi

Re: [gmx-users] Problem configuring openMPI

[Roland Schulz]

you will have to set

LD_LIBRARY_PATH to /home/openmpi/lib

use either setenv or export depending on your shell

Roland

On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur  wrote:

> this time upon executing :
> ./configure\
>--prefix /home/local/gromacs\
>--enable-mpi\
>--program-suffix="_mpi"\
>--disable-nice\
>--enable-shared\
>MPICC=/home/openmpi/mpicc\
>
> it exited with the following error:
>
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rw'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_deregister_object'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_register_objects'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_accept_tmout'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to
> `sfh_sock_open_srv_inet_stm'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_set_buf_size'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_find'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getorigin'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamesweep'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_lam_signal'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to
> `sfh_sock_open_clt_inet_stm'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpstate'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `tprintf'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kpause'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_next'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rev8'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvadd'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiselect'
> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrstore'
> collect2: ld returned 1 exit status
> make[1]: *** [mdrun] Error 1
>
> what is the problem now?- Show quoted text -
>
>
> On Wed, Mar 4, 2009 at 12:43 AM, Mani

Re: [gmx-users] gromacs on itanium2

[Marius Retegan]

Hi,
First I've managed to compile 3.3.1 with Intel 9.1 and assembly loops
for ia64. Then I've tried 3.3.3 and 4.0.4. For both I've got a similar
error:

/bin/sh ../../../../libtool   --mode=compile icc -DHAVE_CONFIG_H -I.
-I../../../../src -I/usr/X11R6/include -I../../../../include
-DGMXLIBDIR=\"/fougeron/home/mretegan/software/gromacs-4.0.4/share/top\"
-I/fougeron/home/mretegan/software/fftw3/include  -O2 -mtune=itanium2
-MT nb_kernel010_ia64_single.lo -MD -MP -MF
.deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo
nb_kernel010_ia64_single.S
 icc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include
-I../../../../include
-DGMXLIBDIR=\"/fougeron/home/mretegan/software/gromacs-4.0.4/share/top\"
-I/fougeron/home/mretegan/software/fftw3/include -O2 -mtune=itanium2
-MT nb_kernel010_ia64_single.lo -MD -MP -MF
.deps/nb_kernel010_ia64_single.Tpo -c nb_kernel010_ia64_single.S -o
nb_kernel010_ia64_single.o
/tmp/iccDePOHl.s(1) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(2) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(3) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(4) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(5) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(6) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(7) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(8) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(10) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(15) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(193) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(195) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(269) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(423) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/iccDePOHl.s(506) : error A2040: Unexpected token: Unary Diez
Operator at: Start
nb_kernel010_ia64_single.o - 15 error(s), 0 warning(s)


After I started looking on the archive and I've found the this thread
http://www.mail-archive.com/gmx-users@gromacs.org/msg16911.html. Then
I've installed the latest Intel compilers (11.0) and I've managed to
get it compiled. Unfortunately when I've tested the build, the complex
test failed without producing any output (not even test FAILED). I
tried to run them by hand, but strangely after I ran the mdrun command
they just kept on running. No error whatsoever.

The fftw were compiled with the same compiler as Gromacs. I've use O2
optimizations in CFLAGS.

Thanks,
Marius

On Tue, Mar 3, 2009 at 8:14 PM, David van der Spoel
 wrote:
> Marius Retegan wrote:
>>
>> Hello
>>
>> Since I was unable to get a working version for Gromacs 4.0.4 on a
>> Itanium 2 machine with the ia64 nonbonded kernel, I was wondering what
>> would be the lost in speed if I would disable the assembly loops?
>>
> About a factor of two. What's the problem with compiling?
>
>> Thanks,
>> Marius
>> ___
>> gmx-users mailing list    gmx-us...@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.se    sp...@gromacs.org   http://folding.bmc.uu.se
> ___
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Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

this time upon executing :
./configure\
   --prefix /home/local/gromacs\
   --enable-mpi\
   --program-suffix="_mpi"\
   --disable-nice\
   --enable-shared\
   MPICC=/home/openmpi/mpicc\

it exited with the following error:

../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append'
../mdlib/.libs/libmd_mpi.so: undefined reference to `rw'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_deregister_object'
../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend'
../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub'
../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4'
../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel'
../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid'
../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom'
../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget'
../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent'
../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry'
../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr'
../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute'
../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes'
../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_register_objects'
../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks'
../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free'
../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete'
../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit'
../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv'
../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init'
../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv'
../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help'
../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime'
../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi'
../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit'
../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_accept_tmout'
../mdlib/.libs/libmd_mpi.so: undefined reference to
`sfh_sock_open_srv_inet_stm'
../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find'
../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert'
../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert'
../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete'
../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_set_buf_size'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand'
../mdlib/.libs/libmd_mpi.so: undefined reference to `al_find'
../mdlib/.libs/libmd_mpi.so: undefined reference to `getorigin'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamesweep'
../mdlib/.libs/libmd_mpi.so: undefined reference to `_lam_signal'
../mdlib/.libs/libmd_mpi.so: undefined reference to
`sfh_sock_open_clt_inet_stm'
../mdlib/.libs/libmd_mpi.so: undefined reference to `rpstate'
../mdlib/.libs/libmd_mpi.so: undefined reference to `tprintf'
../mdlib/.libs/libmd_mpi.so: undefined reference to `kpause'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_next'
../mdlib/.libs/libmd_mpi.so: undefined reference to `rev8'
../mdlib/.libs/libmd_mpi.so: undefined reference to `argvadd'
../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiselect'
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrstore'
collect2: ld returned 1 exit status
make[1]: *** [mdrun] Error 1

what is the problem now?

On Wed, Mar 4, 2009 at 12:43 AM, Manik Mayur  wrote:

>
>
> On Wed, Mar 4, 2009 at 12:28 AM, Nicolas  wrote:
>
>> Manik Mayur a écrit :
>>
>>>
>>>
>>> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas >> nsa...@ucalgary.ca>> wrote:
>>>
>>>Manik Mayur a écrit :
>>>
>>>Hi,
>>>
>>>If I have 2 mpi environments, namely LAM and openMPI, and I
>>>want gromacs to use openMPI of the two

Re: [gmx-users] gromacs on itanium2

[David van der Spoel]

Marius Retegan wrote:

Hello

Since I was unable to get a working version for Gromacs 4.0.4 on a
Itanium 2 machine with the ia64 nonbonded kernel, I was wondering what
would be the lost in speed if I would disable the assembly loops?


About a factor of two. What's the problem with compiling?


Thanks,
Marius
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

On Wed, Mar 4, 2009 at 12:28 AM, Nicolas  wrote:

> Manik Mayur a écrit :
>
>>
>>
>> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas > nsa...@ucalgary.ca>> wrote:
>>
>>Manik Mayur a écrit :
>>
>>Hi,
>>
>>If I have 2 mpi environments, namely LAM and openMPI, and I
>>want gromacs to use openMPI of the two, what extra option
>>should I pass during the ./configure step? In my case openMPI
>>is installed locally(in my /home folder).
>>
>>Sorry, I've misunderstood your message. Anyway, I would first
>>check twice the paths to the binaries in my script. Then, I would
>>check my environment variables, especially PATH, LD_LIBRARY_PATH
>>and LD_RUN_PATH. You might need to modify them to make sure any
>>Lam-related stuff is loaded by default in your environment.
>>
>>
>> ok, is there any specific option or environment variable through which I
>> can make gromacs aware of openMPI and not LAM while installation? If I carry
>> on the default --enable-mpi thing, upon executing the following:
>>
> Just a silly question: Did you recompile Gromacs with openMPI? If not, you
> should with the correct CPPFLAGS, LDFLAGS and MPICC. Typically, you should
> have something like:
>
>   ./configure\
>--prefix /home/local/gromacs\
>--enable-mpi\
>--program-suffix="_mpi"\
>--without-x\
>--disable-nice\
>MPICC=/path/to/mpicc\


thanks, I think that is what I needed. Let me try and then I will let you
know.


>CC=/path/to/gcc
>CPPFLAGS=-I/path/to/fftw/include/\
>LDFLAGS=-L/path/to/fftw/lib/
>

Why is FFTW necessary? In all my gromacs installations till now, I have
avoided this package (out of ignorance).


> mpicc is located in the bin/ directory of openMPI. gcc is the regular gcc
> installation (gcc 3). As I said, your issue is probably due to a path
> uncorrectly pointing to Lam. So check/modify your environment variables,
> especially the paths to loaded libraries.
>
>
>> $/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o
>> eql_mpi.trr
>>
>> I get the following error:
>>
>> 
>>   It seems that there is no lamd running on this host, which
>>   indicates
>>   that the LAM/MPI runtime environment is not operating.  The
>>   LAM/MPI
>>   runtime environment is necessary for MPI programs to run (the MPI
>>   program tired to invoke the "MPI_Init" function).
>>
>>   Please run the "lamboot" command the start the LAM/MPI runtime
>>   environment.  See the LAM/MPI documentation for how to invoke
>>   "lamboot" across multiple machines.
>>
>>   
>> -
>> so it is like mdrun_mpi was configured with LAM and hence it is looking
>> for it.
>>
>>I've tried to use a local installation of openMPI myself, but
>>finally asked my sysadmin to install it for all users. I had many
>>problems with libraries that couldn't be loaded properly.
>>
>>Cheers,
>>Nicolas
>>
>>
>>Thanks,
>>Manik
>>
>>
>>On Tue, Mar 3, 2009 at 10:58 PM, Nicolas > >
>>>> wrote:
>>
>>   Hi,
>>
>>   As mentioned by the error message:
>>
>>
>> Please run the "lamboot" command the start the LAM/MPI
>>runtime
>>
>>   Before using Lam, you have to boot it. In my scripts, I've got
>>   something like:
>>
>> lamboot -v $PBS_NODEFILE
>> lamrun -v -np $NPROC mdrun mdargs
>> lamhalt
>>
>>   I don't use Lam often, though, you might need to use
>>different Lam
>>   options.
>>
>>   Nicolas
>>
>>   Manik Mayur a écrit :
>>
>>   Hi,
>>
>>   I have till now successfully used openMPI and gromacs
>>   together. Recently I got a cluster where I tried to install
>>   openMPI and gromacs locally as I donot have root
>>priviledges
>>   on it. But it turns out that it already has MPI
>>environment on
>>   it (LAM) which I donot want to use (as the version is quite
>>   old.. the cluster still has gcc-3.2.3!).
>>   So after installing openMPI 1.3 and gromacs 4.0.4 on it
>>(in my
>>   /home folder), I tried to execute:
>>
>>   $/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s
>>eql_mpi.tpr -o
>>   eql_mpi.trr
>>
>>   It gives the following error:
>>
>>
>> -
>>   It seems that there is no lamd running on this host, which
>>   indicates
>>   that the LAM/MPI runtime environment is not operating.  The
>>   LAM/MPI
>>   runtime environment is necess

Re: [gmx-users] Problem configuring openMPI

[Nicolas]

Manik Mayur a écrit :



On Tue, Mar 3, 2009 at 11:47 PM, Nicolas > wrote:


Manik Mayur a écrit :

Hi,

If I have 2 mpi environments, namely LAM and openMPI, and I
want gromacs to use openMPI of the two, what extra option
should I pass during the ./configure step? In my case openMPI
is installed locally(in my /home folder).

Sorry, I've misunderstood your message. Anyway, I would first
check twice the paths to the binaries in my script. Then, I would
check my environment variables, especially PATH, LD_LIBRARY_PATH
and LD_RUN_PATH. You might need to modify them to make sure any
Lam-related stuff is loaded by default in your environment.


ok, is there any specific option or environment variable through which 
I can make gromacs aware of openMPI and not LAM while installation? If 
I carry on the default --enable-mpi thing, upon executing the following:
Just a silly question: Did you recompile Gromacs with openMPI? If not, 
you should with the correct CPPFLAGS, LDFLAGS and MPICC. Typically, you 
should have something like:


   ./configure\
--prefix /home/local/gromacs\
--enable-mpi\
--program-suffix="_mpi"\
--without-x\
--disable-nice\
MPICC=/path/to/mpicc\
CC=/path/to/gcc
CPPFLAGS=-I/path/to/fftw/include/\
LDFLAGS=-L/path/to/fftw/lib/
 

mpicc is located in the bin/ directory of openMPI. gcc is the regular 
gcc installation (gcc 3). As I said, your issue is probably due to a 
path uncorrectly pointing to Lam. So check/modify your environment 
variables, especially the paths to loaded libraries.




 $/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o 
eql_mpi.trr


I get the following error:


   It seems that there is no lamd running on this host, which
   indicates
   that the LAM/MPI runtime environment is not operating.  The
   LAM/MPI
   runtime environment is necessary for MPI programs to run (the MPI
   program tired to invoke the "MPI_Init" function).

   Please run the "lamboot" command the start the LAM/MPI runtime
   environment.  See the LAM/MPI documentation for how to invoke
   "lamboot" across multiple machines.
  
 -
so it is like mdrun_mpi was configured with LAM and hence it is 
looking for it.


I've tried to use a local installation of openMPI myself, but
finally asked my sysadmin to install it for all users. I had many
problems with libraries that couldn't be loaded properly.

Cheers,
Nicolas


Thanks,
Manik


On Tue, Mar 3, 2009 at 10:58 PM, Nicolas mailto:nsa...@ucalgary.ca> >> wrote:

   Hi,

   As mentioned by the error message:


 Please run the "lamboot" command the start the LAM/MPI
runtime

   Before using Lam, you have to boot it. In my scripts, I've got
   something like:

 lamboot -v $PBS_NODEFILE
 lamrun -v -np $NPROC mdrun mdargs
 lamhalt

   I don't use Lam often, though, you might need to use
different Lam
   options.

   Nicolas

   Manik Mayur a écrit :

   Hi,

   I have till now successfully used openMPI and gromacs
   together. Recently I got a cluster where I tried to install
   openMPI and gromacs locally as I donot have root
priviledges
   on it. But it turns out that it already has MPI
environment on
   it (LAM) which I donot want to use (as the version is quite
   old.. the cluster still has gcc-3.2.3!).
   So after installing openMPI 1.3 and gromacs 4.0.4 on it
(in my
   /home folder), I tried to execute:

   $/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s
eql_mpi.tpr -o
   eql_mpi.trr

   It gives the following error:

 
 -

   It seems that there is no lamd running on this host, which
   indicates
   that the LAM/MPI runtime environment is not operating.  The
   LAM/MPI
   runtime environment is necessary for MPI programs to
run (the MPI
   program tired to invoke the "MPI_Init" function).

   Please run the "lamboot" command the start the LAM/MPI
runtime
   environment.  See the LAM/MPI documentation for how to
invoke
   "lamboot" across multiple machines.
 
 -


   My question is - Why it

Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

On Tue, Mar 3, 2009 at 11:47 PM, Nicolas  wrote:

> Manik Mayur a écrit :
>
>> Hi,
>>
>> If I have 2 mpi environments, namely LAM and openMPI, and I want gromacs
>> to use openMPI of the two, what extra option should I pass during the
>> ./configure step? In my case openMPI is installed locally(in my /home
>> folder).
>>
> Sorry, I've misunderstood your message. Anyway, I would first check twice
> the paths to the binaries in my script. Then, I would check my environment
> variables, especially PATH, LD_LIBRARY_PATH and LD_RUN_PATH. You might need
> to modify them to make sure any Lam-related stuff is loaded by default in
> your environment.
>

ok, is there any specific option or environment variable through which I can
make gromacs aware of openMPI and not LAM while installation? If I carry on
the default --enable-mpi thing, upon executing the following:

 $/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o eql_mpi.trr

I get the following error:


   It seems that there is no lamd running on this host, which
   indicates
   that the LAM/MPI runtime environment is not operating.  The
   LAM/MPI
   runtime environment is necessary for MPI programs to run (the MPI
   program tired to invoke the "MPI_Init" function).

   Please run the "lamboot" command the start the LAM/MPI runtime
   environment.  See the LAM/MPI documentation for how to invoke
   "lamboot" across multiple machines.

 -
so it is like mdrun_mpi was configured with LAM and hence it is looking for
it.

I've tried to use a local installation of openMPI myself, but finally asked
> my sysadmin to install it for all users. I had many problems with libraries
> that couldn't be loaded properly.
>
> Cheers,
> Nicolas
>
>>
>> Thanks,
>> Manik
>>
>>
>> On Tue, Mar 3, 2009 at 10:58 PM, Nicolas > nsa...@ucalgary.ca>> wrote:
>>
>>Hi,
>>
>>As mentioned by the error message:
>>
>>
>>  Please run the "lamboot" command the start the LAM/MPI runtime
>>
>>Before using Lam, you have to boot it. In my scripts, I've got
>>something like:
>>
>>  lamboot -v $PBS_NODEFILE
>>  lamrun -v -np $NPROC mdrun mdargs
>>  lamhalt
>>
>>I don't use Lam often, though, you might need to use different Lam
>>options.
>>
>>Nicolas
>>
>>Manik Mayur a écrit :
>>
>>Hi,
>>
>>I have till now successfully used openMPI and gromacs
>>together. Recently I got a cluster where I tried to install
>>openMPI and gromacs locally as I donot have root priviledges
>>on it. But it turns out that it already has MPI environment on
>>it (LAM) which I donot want to use (as the version is quite
>>old.. the cluster still has gcc-3.2.3!).
>>So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my
>>/home folder), I tried to execute:
>>
>>$/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o
>>eql_mpi.trr
>>
>>It gives the following error:
>>
>>
>>  
>> -
>>It seems that there is no lamd running on this host, which
>>indicates
>>that the LAM/MPI runtime environment is not operating.  The
>>LAM/MPI
>>runtime environment is necessary for MPI programs to run (the MPI
>>program tired to invoke the "MPI_Init" function).
>>
>>Please run the "lamboot" command the start the LAM/MPI runtime
>>environment.  See the LAM/MPI documentation for how to invoke
>>"lamboot" across multiple machines.
>>
>>  
>> -
>>
>>My question is - Why it still tries to look for LAM
>>environment or lamd? I will be extremely thankful if somebody
>>gives a hint.
>>
>>-Manik
>>--Graduate student
>>Microfluidics Lab
>>Dept. of Mechanical Engg.
>>IIT Kharagpur
>>
>>  
>>
>>___
>>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!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please searc

Re: [gmx-users] Problem configuring openMPI

[Nicolas]

Manik Mayur a écrit :

Hi,

If I have 2 mpi environments, namely LAM and openMPI, and I want 
gromacs to use openMPI of the two, what extra option should I pass 
during the ./configure step? In my case openMPI is installed 
locally(in my /home folder).
Sorry, I've misunderstood your message. Anyway, I would first check 
twice the paths to the binaries in my script. Then, I would check my 
environment variables, especially PATH, LD_LIBRARY_PATH and LD_RUN_PATH. 
You might need to modify them to make sure any Lam-related stuff is 
loaded by default in your environment.


I've tried to use a local installation of openMPI myself, but finally 
asked my sysadmin to install it for all users. I had many problems with 
libraries that couldn't be loaded properly.


Cheers,
Nicolas


Thanks,
Manik

On Tue, Mar 3, 2009 at 10:58 PM, Nicolas > wrote:


Hi,

As mentioned by the error message:


  Please run the "lamboot" command the start the LAM/MPI runtime

Before using Lam, you have to boot it. In my scripts, I've got
something like:

  lamboot -v $PBS_NODEFILE
  lamrun -v -np $NPROC mdrun mdargs
  lamhalt

I don't use Lam often, though, you might need to use different Lam
options.

Nicolas

Manik Mayur a écrit :

Hi,

I have till now successfully used openMPI and gromacs
together. Recently I got a cluster where I tried to install
openMPI and gromacs locally as I donot have root priviledges
on it. But it turns out that it already has MPI environment on
it (LAM) which I donot want to use (as the version is quite
old.. the cluster still has gcc-3.2.3!).
So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my
/home folder), I tried to execute:

$/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o
eql_mpi.trr

It gives the following error:


-
It seems that there is no lamd running on this host, which
indicates
that the LAM/MPI runtime environment is not operating.  The
LAM/MPI
runtime environment is necessary for MPI programs to run (the MPI
program tired to invoke the "MPI_Init" function).

Please run the "lamboot" command the start the LAM/MPI runtime
environment.  See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.

-

My question is - Why it still tries to look for LAM
environment or lamd? I will be extremely thankful if somebody
gives a hint.

-Manik
-- 
Graduate student

Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur


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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur


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begin:vcard
fn:Nicolas Sapay
n:Sapay;Nicolas
org:University of Calgary;Biological department
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:nsa...@ucalgary.ca
title:Post-doctoral fellow
tel;work:403-220-6869
x-mozilla-html:TRUE
url:http://moose.bio.ucalgary.ca/
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[gmx-users] gromacs on itanium2

[Marius Retegan]

Hello

Since I was unable to get a working version for Gromacs 4.0.4 on a
Itanium 2 machine with the ia64 nonbonded kernel, I was wondering what
would be the lost in speed if I would disable the assembly loops?

Thanks,
Marius
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Re: [gmx-users] box size

[Ricardo Soares]

noob noob wrote:


Dear all,

 I am new about MD simulation and I have some questions about the box 
size.


I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 
nm ) but now I change to a bigger molecules and increase the number of 
molecules. So,the new system cannot fix into the previous box. 
Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm 
x 20 nm) which can fix the system nicely.




Hi,
did you use the "-d" option in editconf to create the box size?


So, is it compulsory to use certain box size in our system? or we just use
any box size which our molecules can fix into it, then perform MD?

Sorry for the "stupid" questions.

thanks for the comments.


Alvin Chan.

See all the ways you can stay connected to friends and family 




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--
___

Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
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Re: [gmx-users] simulation box

[Justin A. Lemkul]

Quoting Ricardo Soares :

> noob noob wrote:
> >
> > Dear all,
> >
> >  I am new about MD simulation and I have some questions about the box
> > size.
> >
> > I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5
> > nm ) but now I change to a bigger molecules and increase the number of
> > molecules. So,the new system cannot fix into the previous box.
> > Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm
> > x 20 nm) which can fix the system nicely.
> >
> > So, is it compulsory to use certain box size in our system? or we just use
> > any box size which our molecules can fix into it, then perform MD?
> >
> Sorry, I didn't see this other question of yours.
> If you use a box that is much larger than the main molecule, you will
> need lots of water, which will be time-consuming. Otherwise, if you use
> a very small box, it may compromise the free movement of the protein.
> So i say the best option is to scale the box size according to your
> specific molecule size. This is done within the editconf program. (see
> the gromacs manual for further reference).
>

In addition, you need to consider cutoff lengths and periodic boundary
conditions/minimum image convention.  Some textbook reading is in order.

-Justin

> Cheers,
>
> Ricardo.
>
>
> > Sorry for the "stupid" questions.
> >
> > thanks for the comments.
> >
> >
> > Alvin Chan.
> > 
> > check out the rest of the Windows Live™. More than mail–Windows Live™
> > goes way beyond your inbox. More than messages
> > 
> > 
> >
> > ___
> > 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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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> ___
>
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___
>
> ___
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>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem...@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] Problem configuring openMPI

[Manik Mayur]

Hi,

If I have 2 mpi environments, namely LAM and openMPI, and I want gromacs to
use openMPI of the two, what extra option should I pass during the
./configure step? In my case openMPI is installed locally(in my /home
folder).

Thanks,
Manik

On Tue, Mar 3, 2009 at 10:58 PM, Nicolas  wrote:

> Hi,
>
> As mentioned by the error message:
>
>   Please run the "lamboot" command the start the LAM/MPI runtime
>
> Before using Lam, you have to boot it. In my scripts, I've got something
> like:
>
>   lamboot -v $PBS_NODEFILE
>   lamrun -v -np $NPROC mdrun mdargs
>   lamhalt
>
> I don't use Lam often, though, you might need to use different Lam options.
>
> Nicolas
>
> Manik Mayur a écrit :
>
>> Hi,
>>
>> I have till now successfully used openMPI and gromacs together. Recently I
>> got a cluster where I tried to install openMPI and gromacs locally as I
>> donot have root priviledges on it. But it turns out that it already has MPI
>> environment on it (LAM) which I donot want to use (as the version is quite
>> old.. the cluster still has gcc-3.2.3!).
>> So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my /home
>> folder), I tried to execute:
>>
>> $/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o eql_mpi.trr
>>
>> It gives the following error:
>>
>>
>> -
>> It seems that there is no lamd running on this host, which indicates
>> that the LAM/MPI runtime environment is not operating.  The LAM/MPI
>> runtime environment is necessary for MPI programs to run (the MPI
>> program tired to invoke the "MPI_Init" function).
>>
>> Please run the "lamboot" command the start the LAM/MPI runtime
>> environment.  See the LAM/MPI documentation for how to invoke
>> "lamboot" across multiple machines.
>>
>> -
>>
>> My question is - Why it still tries to look for LAM environment or lamd? I
>> will be extremely thankful if somebody gives a hint.
>>
>> -Manik
>> --
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> 
>>
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>> Please search the archive at http://www.gromacs.org/search before
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>
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-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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Re: [gmx-users] simulation box

[Ricardo Soares]

noob noob wrote:


Dear all,

 I am new about MD simulation and I have some questions about the box 
size.


I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 
nm ) but now I change to a bigger molecules and increase the number of 
molecules. So,the new system cannot fix into the previous box. 
Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm 
x 20 nm) which can fix the system nicely.


So, is it compulsory to use certain box size in our system? or we just use
any box size which our molecules can fix into it, then perform MD?


Sorry, I didn't see this other question of yours.
If you use a box that is much larger than the main molecule, you will 
need lots of water, which will be time-consuming. Otherwise, if you use 
a very small box, it may compromise the free movement of the protein.
So i say the best option is to scale the box size according to your 
specific molecule size. This is done within the editconf program. (see 
the gromacs manual for further reference).


Cheers,

Ricardo.



Sorry for the "stupid" questions.

thanks for the comments.


Alvin Chan.

check out the rest of the Windows Live™. More than mail–Windows Live™ 
goes way beyond your inbox. More than messages 




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--
___

Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
___

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Re: [gmx-users] Problem configuring openMPI

[Nicolas]

Hi,

As mentioned by the error message:

   Please run the "lamboot" command the start the LAM/MPI runtime

Before using Lam, you have to boot it. In my scripts, I've got something 
like:


   lamboot -v $PBS_NODEFILE
   lamrun -v -np $NPROC mdrun mdargs
   lamhalt

I don't use Lam often, though, you might need to use different Lam options.

Nicolas

Manik Mayur a écrit :

Hi,

I have till now successfully used openMPI and gromacs together. 
Recently I got a cluster where I tried to install openMPI and gromacs 
locally as I donot have root priviledges on it. But it turns out that 
it already has MPI environment on it (LAM) which I donot want to use 
(as the version is quite old.. the cluster still has gcc-3.2.3!).
So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my /home 
folder), I tried to execute:


$/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o eql_mpi.trr

It gives the following error:

-
It seems that there is no lamd running on this host, which indicates
that the LAM/MPI runtime environment is not operating.  The LAM/MPI
runtime environment is necessary for MPI programs to run (the MPI
program tired to invoke the "MPI_Init" function).

Please run the "lamboot" command the start the LAM/MPI runtime
environment.  See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-

My question is - Why it still tries to look for LAM environment or 
lamd? I will be extremely thankful if somebody gives a hint.


-Manik
--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur


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n:Sapay;Nicolas
org:University of Calgary;Biological department
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
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[gmx-users] simulation box

[noob noob]

Dear all,

 I am new about MD simulation and I have some questions about the box size.

I
had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm
) but now I change to a bigger molecules and increase the number of
molecules. So,the new system cannot fix into the previous box.
Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm x
20 nm) which can fix the system nicely. 

So, is it compulsory to use certain box size in our system? or we just use
any box size which our molecules can fix into it, then perform MD?

Sorry for the "stupid" questions.

thanks for the comments.


Alvin Chan.
_
More than messages–check out the rest of the Windows Live™.
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[gmx-users] box size

[noob noob]

Dear all,

 I am new about MD simulation and I have some questions about the box size.

I
had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm
) but now I change to a bigger molecules and increase the number of
molecules. So,the new system cannot fix into the previous box.
Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm x
20 nm) which can fix the system nicely. 

So, is it compulsory to use certain box size in our system? or we just use
any box size which our molecules can fix into it, then perform MD?

Sorry for the "stupid" questions.

thanks for the comments.


Alvin Chan.
_
See all the ways you can stay connected to friends and family
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[gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

[Claus Valka]

Hello,
this has to do with my personal experience of using Gromacs version 4.0.3. So 
this is not an official response.
The story:
While I was trying to run an NVT simulation in a monoclinic box I encountered 
the following problem:
Fatal error:
25 of the 336080 bonded interactions could not be calculated because some atoms 
involved moved further apart than the multi-body cut-off distance (0.895 nm) or 
the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and 
tabulated bonds also see option -ddcheck

and the:
Not all bonded interactions have been properly assigned to the domain 
decomposition cells

Trying to put aside the fact that my system had any bug I found in the net the 
following:
http://www.gromacs.org/pipermail/gmx-developers/2008-January/002373.html

In order to overcome this error I increased the value of
table-extension  = 30
in my mdp file in such a way, as to be bigger from my biggest dimension I had 
in my system. The ran proceeded (until now that I'm writing this e-mail) 
without any problem.

This value has to do with the cut-off of pairs1-4 LJ interactions and is 
calculated in nm.

JFYI
Regards,
Nikos






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Re: [gmx-users] gromacs-4.0.2, parallel performance in two quadcore xeon machines

[Antoine FORTUNE]

Hi Nikos,

I experienced the same king of things with a core i7 on one node and a
corequad on an second node (Gromacs 4.0.3).
Running on 8 threads (i7) or 4 cores in a single node is 30% faster than
8 or 12 "cores" on 2 nodes. I noticed that my gigabit switch is not
limiting bandwidth using openmpi with rsh (~30 Gbps/70 max).
Running on a single node cpu is 100% used by user (mdruns) while using 2
nodes each cpu is only 50% used by user, the 50% remaining being used by
system. The top command shows 4 mdrun jobs using 100% CPU.
I guess system usage is for network transferts ... Using ssh, system
usage is quite the same and bandwidth is doubled.

Any ideas about that system activity and how to reduce it ?

Thanks



Berk Hess a écrit :
> Hi,
>
> Oops, I meant 72000, which is only a factor of 10.
> I guess it might be faster one two nodes then, but probably not 2 times.
> If you use PME you can also experiment with putting all the PME nodes
> on one machine and the non-PME nodes on the other,
> probably with mdrun -ddorder pp_pme
>
> Gromacs supports near to maxint atoms.
> The question is much more what kind of system size you are
> scientifically interested in.
>
> Ethernet will never scale very well for small numbers of atoms per core.
> Infiniband will scale very well.
>
> Berk
>
>
> 
> Date: Wed, 18 Feb 2009 12:56:16 -0800
> From: lastexile...@yahoo.de
> Subject: RE: [gmx-users] gromacs-4.0.2, parallel performance in two
> quad core xeon machines
> To: gmx-users@gromacs.org
>
> Hello,
>
> thank you for your answer. I just wondering though. How am I supposed
> to have a system with more than 9 atoms, while the gro file has a
> fixed format giving up to 5 digits in the number of atoms? 
>
>
> What else should I change in order to succeed better performance from
> my hardware if I can succeed having a much bigger system? You say so
> that ethernet has reached its limits.. 
>
> I was concidering using a supercomputing center in Europe and as far
> as I know they are using nodes which are using the Cell 9 core
> processors technology in each node. How someone there can accomplish a
> better performance using gromacs 4 using more nodes? Which might be
> the limit there in such machines.  
>
> Thank you once again,
> Nikos
>
> --- Berk Hess // schrieb am *Mi, 18.2.2009:
> *
>
> *Von: Berk Hess 
> Betreff: RE: [gmx-users] gromacs-4.0.2, parallel performance in
> two quad core xeon machines
> An: lastexile...@yahoo.de
> Datum: Mittwoch, 18. Februar 2009, 19:16
>
> *
> * Hi,
>
> You can not scale a system of just 7200 atoms
> to 16 cores which are connected by ethernet.
> 400 atoms per core is already the scaling limit of Gromacs
> on current hardware with the fastest available network.
>
> On ethernet a system 100 times as large might scale well to two nodes.
>
> Berk
>
>
> *
> 
> *Date: Wed, 18 Feb 2009 09:40:28 -0800
> From: lastexile...@yahoo.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] gromacs-4.0.2, parallel performance in two
> quad core xeon machines
>
> *
> Hello,
>
> we have built a cluster with nodes that are comprised by the
> following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The
> memory of each node has 16Gb of memory. The switch that we use is
> a dell power connect model. Each node has a Gigabyte ethernet card..
>
> I tested the performance for a system of 7200 atoms in 4cores of
> one node, in 8 cores of one node and in 16 cores of two nodes. In
> one node the performance is getting better.
> The problem I get is that moving from one node to two, the
> performance decreases dramatically (almost two days for a run that
> finishes in less than 3 hours!).
>
> I have compiled gromacs with --enable-mpi option. I also have read
> previous archives from Mr Kurtzner, yet from what I saw is that
> they are focused on errors in gromacs 4 or on problems that
> previous versions of gromacs had. I get no errors, just low
> performance.
>
> Is there any option that I must enable in order to succeed better
> performance in more than one nodes?  Or do you think according to
> your experience that the switch we use might be the problem? Or
> maybe should we have to activate anything from the nodes?
>
> Thank you in advance,
> Nikos
>
> *
>
> *
> 
> *Express yourself instantly with MSN Messenger! MSN Messenger
>  *
>
>
>
> 
> Express yourself instantly with MSN Messenger! MSN Messenger
> 
> 

[gmx-users] Problem configuring openMPI

[Manik Mayur]

Hi,

I have till now successfully used openMPI and gromacs together. Recently I
got a cluster where I tried to install openMPI and gromacs locally as I
donot have root priviledges on it. But it turns out that it already has MPI
environment on it (LAM) which I donot want to use (as the version is quite
old.. the cluster still has gcc-3.2.3!).
So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my /home
folder), I tried to execute:

$/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o eql_mpi.trr

It gives the following error:

-
It seems that there is no lamd running on this host, which indicates
that the LAM/MPI runtime environment is not operating.  The LAM/MPI
runtime environment is necessary for MPI programs to run (the MPI
program tired to invoke the "MPI_Init" function).

Please run the "lamboot" command the start the LAM/MPI runtime
environment.  See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-

My question is - Why it still tries to look for LAM environment or lamd? I
will be extremely thankful if somebody gives a hint.

-Manik
-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Justin A. Lemkul]

Chansoo Kim wrote:

Dear Justin:


Please call me, 'chance'. 
I have been doing neutron scattering and MD on water. 
Thank you again for this conversation with you, Justin.


Right now, I am trying to do polymer simulation to mimic an interaction 
with a plasma.

To do so, I am targeting PE system.

Related to the my question related to the [Error] and [Question #1],

 [Error]
 When I did run the pdb2gmx, I got the following error.
 "Atom -C2 not found in residue PEth1 while adding hydrogens"



You can't specify a previous residue (designated by -) from the first residue in 
a chain.  Hence why I suggested what I did before about special terminal 
residues.  See the post I just sent about functioning .rtp and .hdb entries, 
they worked for me.


-Justin


 [Question #1]
 Therefore, what I should define more...?

I cannot avoid to ask you this question again!

As I emailed you, since I corrected error related to "blank" in the 
input files (pdb and etc.), it has never given me "segmentation fault."

The only error that the gromacs gives me is the above one.

Even though I am following your suggestion in the previous email, I want 
to clarify the above problem.


Do you have any idea on this...?

Thank you again!!


Sincerely yours,

Chance


(PS) The "chemical reaction", which I wrote in the second email, is my 
mistake. I did not mean "chemical reaction"... And I appreciate that you 
pointed it out.




On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul > wrote:




Chansoo Kim wrote:

Dear Justin:


Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..)
work, but I do not clearly understand chemical reaction, which I
have to define in those files...


No chemical reactions occur :)  See comments embedded below



[Situation]
I want to do simulate polyethylene (PE) using Gromacs and
OPLS-AA force field...

[Topology files and etc]
 (1) rtp file

[ Eth ]
 [ atoms ]
  C1opls_136-0.1201
  H11   opls_140 0.0601
  H12   opls_140 0.0601
  C2opls_136-0.1202
  H21   opls_140 0.0602
  H22   opls_140 0.0602
 [ bonds ]
  C1H11
  C1H12
  C1C2
  C2H21
  C2H22
  C2+C1


 (2) hdb file
Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


 (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
opls_140   1.008   0.06
[ delete ]
H21
H22


 (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
opls_140   1.008   0.06
[ delete ]
H21
H22


Note that the message you referenced in your first post (which
provided you with this .rtp entry) resulted in a segmentation fault,
therefore indicating that it probably won't work.



  (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


+ means next residue, - means previous.




[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my
terminal did NOT work...).
And those positions are all (0, 0, 0).


Right, because H positioning in a polymer chain may depend on
previous (-) or subsequent (+) residues, so the code doesn't know
where to put them.


Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Justin A. Lemkul]

I took a few minutes to look into this.  Since I have seen these same, 
incomplete posts that give no solution, let me propose one.  I was able to 
produce an OPLS-AA PE topology with pdb2gmx using the following additions to the 
corresponding .rtp and .hdb files:


ffoplsaa.rtp:

; Polyethylene - this is an internal residue
[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1-C2
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1

; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ EthB ]
 [ atoms ]
   C1opls_135-0.1801
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   H13   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1H13
   C1C2
   C2H21
   C2H22
   C2+C1

; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_135-0.1802
   H21   opls_140 0.0602
   H22   opls_140 0.0602
   H23   opls_140 0.0602
 [ bonds ]
   C1-C2
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2H23

ffoplsaa.hdb:

Eth 2
2   6   H1  C1  C2  -C2
2   6   H2  C2  C1  +C1
EthB2
3   4   H1  C1  C2  +C1
2   6   H2  C2  C1  +C1
EthE2
2   6   H1  C1  C2  -C2
3   4   H2  C2  C1  -C2 

I successfully created a topology from pdb2gmx using this .pdb file:

ATOM  1  C1  EthB1   1.000   1.540   0.000
ATOM  2  C2  EthB1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  EthE3   3.912   5.623   0.000
ATOM  6  C2  EthE3   5.368   6.124   0.000
END

I think the main reason the -n.tdb and -c.tdb modifications do not work is the 
following message from pdb2gmx: "No N- or C-terminus found: this chain appears 
to contain no protein."


I do not vouch for the validity of these parameters, as I have no need to test 
them.  This information is only meant to be instructive regarding using pdb2gmx 
to generate a topology; it is an exercise for the user to determine whether or 
not such parameters are valid.


-Justin

Zuzana Benkova wrote:

Dear Chansoo Kim,

It has passed relatively long time since I attempted to use pdb2gmx to 
build my topology for polyethylene. I prepared the relevant files 
according to those used for amino acids. I used + and – sign to discern 
the direction of connectivity. I have encountered dome problems 
mentioned in the mail but they have not been answered satisfactorily. 
Later on I wanted to run just united atom simulations and I had next 
problem with pdb2gmx that always include hydrogen atoms to my topology 
though I used option which should have disabled this. I decided to build 
my topology file without pdb2gmx and I applied force field that is not 
present in GMX directories.


 




*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Chansoo Kim

*Sent:* Tuesday, March 03, 2009 2:50 PM
*To:* jalem...@vt.edu; Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - 
please!


 


Dear Justin:

 

 


Thank you for your reply.

I was too urgent, so I did not clarify my questions.

Sorry about that.

 

I totally understand how topology files (tdb, hdb, and etc..) work, but 
I do not clearly understand chemical reaction, which I have to define in 
those files...


 

 


*[Situation]*

I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force 
field...


 


*[Topology files and etc]*

  (1) rtp file

[ Eth ]

 [ atoms ]

   C1opls_136-0.1201

   H11   opls_140 0.0601

   H12   opls_140 0.0601

   C2opls_136-0.1202

   H21   opls_140 0.0602

   H22   opls_140 0.0602

 [ bonds ]

   C1H11

   C1H12

   C1C2

   C2H21

   C2H22

   C2+C1

 


  (2) hdb file

Eth 2

2   6   H1   C1  C2 +C1

2   6   H2   C2  C1 -C2

 

 


  (3) -c.tdb file

 


[ Eth ]

[ replace ]

C1  opls_13512.011  -0.18

[ add ]

34  H1  C1  C2

 opls_140   1.008   0.06

[ delete ]

H21

H22

 

 


  (4) -n.tdb file

 


[ Eth ]

[ replace ]

C2  opls_13512.011   -0.18

[ add ]

34  H2  C2  C1

 o

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Chansoo Kim]

Dear Justin and gmx-users:

Thank you for your answer, Justin.

Since I corrected error related to "blank" in the input files (pdb and
etc.), it has never given me "segmentation fault."
So... this problem is not related to this one anyway.

Now, I will try to correct others by following your suggestion.

After trying, I will contact you again... :)

Thank you again!!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul  wrote:

>
>
> Chansoo Kim wrote:
>
>> Dear Justin:
>>
>>
>> Thank you for your reply.
>> I was too urgent, so I did not clarify my questions.
>> Sorry about that.
>>
>> I totally understand how topology files (tdb, hdb, and etc..) work, but I
>> do not clearly understand chemical reaction, which I have to define in those
>> files...
>>
>>
> No chemical reactions occur :)  See comments embedded below
>
>
>
>> [Situation]
>> I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
>> field...
>>
>> [Topology files and etc]
>>  (1) rtp file
>>
>> [ Eth ]
>>  [ atoms ]
>>   C1opls_136-0.1201
>>   H11   opls_140 0.0601
>>   H12   opls_140 0.0601
>>   C2opls_136-0.1202
>>   H21   opls_140 0.0602
>>   H22   opls_140 0.0602
>>  [ bonds ]
>>   C1H11
>>   C1H12
>>   C1C2
>>   C2H21
>>   C2H22
>>   C2+C1
>>
>>
>>  (2) hdb file
>> Eth 2
>> 2   6   H1   C1  C2 +C1
>> 2   6   H2   C2  C1 -C2
>>
>>
>>  (3) -c.tdb file
>>
>> [ Eth ]
>> [ replace ]
>> C1  opls_13512.011  -0.18
>> [ add ]
>> 34  H1  C1  C2
>> opls_140   1.008   0.06
>> [ delete ]
>> H21
>> H22
>>
>>
>>  (4) -n.tdb file
>>
>> [ Eth ]
>> [ replace ]
>> C2  opls_13512.011   -0.18
>> [ add ]
>> 34  H2  C2  C1
>> opls_140   1.008   0.06
>> [ delete ]
>> H21
>> H22
>>
>>
> Note that the message you referenced in your first post (which provided you
> with this .rtp entry) resulted in a segmentation fault, therefore indicating
> that it probably won't work.
>
>
>>   (5) input pdb file
>>
>> ATOM 1 C1 Eth 1 1.000 1.540 0.000
>>
>> ATOM  2  C2  Eth 1   2.456   2.041   0.000
>> ATOM  3  C1  Eth 2   2.456   3.581   0.000
>> ATOM  4  C2  Eth 2   3.912   4.083   0.000
>> ATOM  5  C1  Eth 3   3.912   5.623   0.000
>> ATOM  6  C2  Eth 3   5.368   6.124   0.000
>> END
>>
>>
>> [Error]
>> When I did run the pdb2gmx, I got the following error.
>> "Atom -C not found in residue PEth1 while adding hydrogens"
>>
>> [Question #1 and #2]
>> Therefore, what I should define more...?
>> What does the "+" and "-" mean here?
>>
>
> + means next residue, - means previous.
>
>
>>
>> [If...]
>> If I change the hdb file as follows,
>>
>> Eth 2
>> 2   6   H1   C1  C2 C1
>> 2   6   H2   C2  C1 C2
>>
>>
>> After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did
>> NOT work...).
>> And those positions are all (0, 0, 0).
>>
>>
> Right, because H positioning in a polymer chain may depend on previous (-)
> or subsequent (+) residues, so the code doesn't know where to put them.
>
>
>  Following is the results,
>>
>> LE Giving Russians Opium May Alter Current Situation
>> MODEL1
>> ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
>> ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
>> ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
>> ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
>> ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
>> ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
>> ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
>> ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
>> ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
>> ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
>> TER
>> ENDMDL
>>
>> [Question #3 from If... section ]
>> I guess that I have to change hdb and tdb files.
>> Would you please give some guide on that...?
>>
>>
> Knowing that many people have tried to define PE with .tdb entries (and I
> think success is limited), I would suggest the following.  Define distinct
> .rtp entries for the caps of your chain.  Don't bother with -n.tdb and
> -c.tdb; I d

RE: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Zuzana Benkova]

Dear Chansoo Kim,

It has passed relatively long time since I attempted to use pdb2gmx to build
my topology for polyethylene. I prepared the relevant files according to
those used for amino acids. I used + and - sign to discern the direction of
connectivity. I have encountered dome problems mentioned in the mail but
they have not been answered satisfactorily. Later on I wanted to run just
united atom simulations and I had next problem with pdb2gmx that always
include hydrogen atoms to my topology though I used option which should have
disabled this. I decided to build my topology file without pdb2gmx and I
applied force field that is not present in GMX directories. 

 

  _  

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Chansoo Kim
Sent: Tuesday, March 03, 2009 2:50 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

 

Dear Justin:

 

 

Thank you for your reply.

I was too urgent, so I did not clarify my questions.

Sorry about that.

 

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...

 

 

[Situation]

I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

 

[Topology files and etc]

  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1
 
  (2) hdb file
Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2

 

 
  (3) -c.tdb file
 
[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22

 

 
  (4) -n.tdb file
 
[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22

 

   (5) input pdb file

 

ATOM  1  C1  Eth 1   1.000   1.540   0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END

 

[Error]

When I did run the pdb2gmx, I got the following error.

"Atom -C not found in residue PEth1 while adding hydrogens"

 

[Question #1 and #2]

Therefore, what I should define more...?

What does the "+" and "-" mean here?

 

 

[If...]

If I change the hdb file as follows,

 

 
Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2

 

After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).

And those positions are all (0, 0, 0).

 

Following is the results,

 

LE Giving Russians Opium May Alter Current Situation

MODEL1

ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00

ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00

ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00

ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00

ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00

ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00

ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00

ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00

ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00

ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00

TER

ENDMDL

 

[Question #3 from If... section ]

I guess that I have to change hdb and tdb files.

Would you please give some guide on that...?

 

Thank you for your care!

 

 

Sincerely yours,

 

C Kim

 

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul  wrote:



Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be not
that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
to tackle my problems.
Sorry to say, I

Re: [gmx-users] add zinc in gromacs/cpmd

[Marius Retegan]

Hi Jacopo,

Find the file qm_cpm.c in src/mdlib and add your parameters at line
353. You will need some parameters for zinc.
I've used the following parameters, but I didn't test the influence on
the obtained results:

  case 30: {
strncpy(qmmm_data->atomdata[i].atomstr,"Zn",
sizeof(qmmm_data->atomdata[i].atomstr));
qmmm_data->asize[i] =  1/2.476; /*  Covalent radius
(this is in atomic units) I took the value from Wikipedia  */
qmmm_data->qcore[i] =  1.86648; } break; /* 1.86648 =
5.6^0.; 5.6=polarizability from Handbook of Chemistry and
Physics*/

Marius

On Tue, Mar 3, 2009 at 2:33 PM, Jacopo Sgrignani
 wrote:
> In the list i found infos about an error i can find working
> with gromacs/cpmd, the Zinc atom is not in the source code.
> Can anybody help me to what number i have to put in the codo to correctly
> add this atom.
>
> Thanks
>
> Jacopo
>
> ___
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Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Justin A. Lemkul]

Chansoo Kim wrote:

Dear Justin:


Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..) work, but 
I do not clearly understand chemical reaction, which I have to define in 
those files...




No chemical reactions occur :)  See comments embedded below



[Situation]
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force 
field...


[Topology files and etc]
  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1


  (2) hdb file
Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


  (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


  (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22



Note that the message you referenced in your first post (which provided you with 
this .rtp entry) resulted in a segmentation fault, therefore indicating that it 
probably won't work.




   (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


+ means next residue, - means previous.




[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did 
NOT work...).

And those positions are all (0, 0, 0).



Right, because H positioning in a polymer chain may depend on previous (-) or 
subsequent (+) residues, so the code doesn't know where to put them.



Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
TER
ENDMDL

[Question #3 from If... section ]
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?



Knowing that many people have tried to define PE with .tdb entries (and I think 
success is limited), I would suggest the following.  Define distinct .rtp 
entries for the caps of your chain.  Don't bother with -n.tdb and -c.tdb; I 
don't know how well the Gromacs code handles non-protein termini (maybe it 
works, but it seems to give fits for polymers).  The .rtp entry for PE you've 
shown above seems reasonable enough for a PE monomer within the chain, but may 
require some tweaking (since I've never tried, I don't know).


-Justin


Thank you for your care!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul > wrote:




Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it
could be not that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users
mailing list to tackle my problems.
 

[gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Chansoo Kim]

Oops...I am truly sorry to bother your mailbox again...
Please understand this beginner...

Error message was, ""Atom -C2 not found in residue PEth1 while adding
hydrogens"

-- Forwarded message --
From: Chansoo Kim 
Date: Tue, Mar 3, 2009 at 8:49 AM
Subject: Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!
To: jalem...@vt.edu, Discussion list for GROMACS users <
gmx-users@gromacs.org>


Dear Justin:

Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...


[Situation]
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

[Topology files and etc]
  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1


  (2) hdb fileEth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


  (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


  (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22


   (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).
And those positions are all (0, 0, 0).

Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
TER
ENDMDL

[Question #3 from If... section ]
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?

Thank you for your care!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul  wrote:

>
>
> Chansoo Kim wrote:
>
>> Dear Dr. Benkova and others:
>>
>>
>> I am C. Kim and trying to simulation polymer system.
>>
>> Since I guessed that polyethylene (PE) is a simple system, it could be not
>> that hard to simulate it in Gromacs.
>> Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
>> to tackle my problems.
>> Sorry to say, I could not solve problems, so I am asking your help!
>>
>> Actually I have used your files written in followings,
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html
>>
>> [Q1]
>> After getting the result from the pdb2gmx, I could not see any H-atoms in
>> my system.
>> All the H-atoms have 0, 0, 0 positions!
>> Therefore, my question is
>>   how I should define hdb?
>>
>
> The .hdb file format is explained in the manual.
>
>
>> [Q2]
>> When I use -C2, and +C1 in hdb file, I always meet error.
>>
>
> What is the error?
>
> -Justin
>
>  Is there any other things to add to the ffopls*.* files...?
>>
>> Thank y

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Chansoo Kim]

Dear Justin:

Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...


[Situation]
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

[Topology files and etc]
  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1


  (2) hdb fileEth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


  (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


  (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22


   (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).
And those positions are all (0, 0, 0).

Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
TER
ENDMDL

[Question #3 from If... section ]
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?

Thank you for your care!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul  wrote:

>
>
> Chansoo Kim wrote:
>
>> Dear Dr. Benkova and others:
>>
>>
>> I am C. Kim and trying to simulation polymer system.
>>
>> Since I guessed that polyethylene (PE) is a simple system, it could be not
>> that hard to simulate it in Gromacs.
>> Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
>> to tackle my problems.
>> Sorry to say, I could not solve problems, so I am asking your help!
>>
>> Actually I have used your files written in followings,
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html
>>
>> [Q1]
>> After getting the result from the pdb2gmx, I could not see any H-atoms in
>> my system.
>> All the H-atoms have 0, 0, 0 positions!
>> Therefore, my question is
>>   how I should define hdb?
>>
>
> The .hdb file format is explained in the manual.
>
>
>> [Q2]
>> When I use -C2, and +C1 in hdb file, I always meet error.
>>
>
> What is the error?
>
> -Justin
>
>  Is there any other things to add to the ffopls*.* files...?
>>
>> Thank you for your care!
>>
>>
>> Sincerely
>> C. Kim
>>
>>
>> 
>>
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. 

[gmx-users] add zinc in gromacs/cpmd

[Jacopo Sgrignani]

In the list i found infos about an error i can find working
with gromacs/cpmd, the Zinc atom is not in the source code.
Can anybody help me to what number i have to put in the codo to correctly
add this atom.

Thanks

Jacopo

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Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Justin A. Lemkul]

Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be 
not that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing 
list to tackle my problems.

Sorry to say, I could not solve problems, so I am asking your help!

Actually I have used your files written in followings,

http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html

[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms 
in my system.

All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
   how I should define hdb?


The .hdb file format is explained in the manual.



[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.


What is the error?

-Justin


Is there any other things to add to the ffopls*.* files...?

Thank you for your care!


Sincerely 


C. Kim




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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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] Fwd: Polyethylene (PE) simulations in Gromacs - please!

[Chansoo Kim]

-- Forwarded message --
From: Chansoo Kim 
Date: Tue, Mar 3, 2009 at 8:28 AM
Subject: Polyethylene (PE) simulations in Gromacs - please!
To: gmx-users@gromacs.org


Dear Dr. Benkova and others:

I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be not
that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
to tackle my problems.
Sorry to say, I could not solve problems, so I am asking your help!

Actually I have used your files written in followings,

http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html

[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms in my
system.
All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
   how I should define hdb?

[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.
Is there any other things to add to the ffopls*.* files...?

Thank you for your care!


Sincerely

C. Kim
___
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Polyethylene (PE) simulations in Gromacs - please!

[Chansoo Kim]

Dear Dr. Benkova and others:

I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be not
that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
to tackle my problems.
Sorry to say, I could not solve problems, so I am asking your help!

Actually I have used your files written in followings,

http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html

[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms in my
system.
All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
   how I should define hdb?

[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.
Is there any other things to add to the ffopls*.* files...?

Thank you for your care!


Sincerely

C. Kim
___
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Re: [gmx-users] regarding dimethylated lysine topology file

[Antonia Vyrkou]

I thing the the function is not written well... It is:
Vd=k_phi(1+cos(n*phi-phi_eq))

Antonia





>prasun kumar  said:

> --000e0cd20d869ab935046434ec49
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: 7bit
> 
> Respected all
> I drew the structure using the drawing tool available in PRODRG server
> then I went for  topology file generation,but the server is deleting almost
> all the hydrogen atoms while writing the topology file for gromacs
> can any one tell me why it is doing like this?
> 
> another question I got that is
> how to change gromacs topology file to charmm topology file
> (I know for bond length and anglebut for dihedral(improper and
> proper))
> actually i want toi know which function gromacs is using for the calculation
> of dihedrals..
> thanx in advance
> 
> PRASUN (ASHOKA)
> 
> --000e0cd20d869ab935046434ec49
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> 
> Respected all I drew the structure using the drawing tool available in =
> PRODRG serverthen I went for=A0 topology file generation,but the server=
>  is deleting almost all the hydrogen atoms while writing the topology file =
> for gromacs
> can any one tell me why it is doing like this?another question I go=
> t that ishow to change gromacs topology file to charmm topology file  r>(I know for bond length and anglebut for dihedral(improper and pr=
> oper))
> actually i want toi know which function gromacs is using for the calculatio=
> n of dihedrals..thanx in advancePRASUN (A=
> SHOKA)
> 
> --000e0cd20d869ab935046434ec49--
> 



-- 



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Re: [gmx-users] regarding dimethylated lysine topology file

[Antonia Vyrkou]

Hi, 

the function used by GROMACS is Vd (öijkl ) = kö (1 + cos(nö − ös )), for
proper dihedrals (periodic type).
Take a look at Chapter 4, of GROMACS-4-0 manual.

Antonia



>prasun kumar  said:

> --000e0cd20d869ab935046434ec49
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: 7bit
> 
> Respected all
> I drew the structure using the drawing tool available in PRODRG server
> then I went for  topology file generation,but the server is deleting almost
> all the hydrogen atoms while writing the topology file for gromacs
> can any one tell me why it is doing like this?
> 
> another question I got that is
> how to change gromacs topology file to charmm topology file
> (I know for bond length and anglebut for dihedral(improper and
> proper))
> actually i want toi know which function gromacs is using for the calculation
> of dihedrals..
> thanx in advance
> 
> PRASUN (ASHOKA)
> 
> --000e0cd20d869ab935046434ec49
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> 
> Respected all I drew the structure using the drawing tool available in =
> PRODRG serverthen I went for=A0 topology file generation,but the server=
>  is deleting almost all the hydrogen atoms while writing the topology file =
> for gromacs
> can any one tell me why it is doing like this?another question I go=
> t that ishow to change gromacs topology file to charmm topology file  r>(I know for bond length and anglebut for dihedral(improper and pr=
> oper))
> actually i want toi know which function gromacs is using for the calculatio=
> n of dihedrals..thanx in advancePRASUN (A=
> SHOKA)
> 
> --000e0cd20d869ab935046434ec49--
> 



-- 



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[gmx-users] (no subject)

[Antonia Vyrkou]

Hello,

I am trying to simulate a system for which I need to exclude all
intramolecular culombic interactions except those included in the pair_list. 
How can I do that?
Also, the pairs defined at the [ pairs ] section are used for both
Lennard-Jones and coulombic interaction, are they not?

Thank you for your help
Antonia
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[gmx-users] (no subject)

[Antonia Vyrkou]

Hello,

I am trying to simulate a system for which I need to exclude all
intramolecular culombic interactions except those included in the pair_list. 
How can I do that?
Also, the pairs defined at the [ pairs ] section are used for both
Lennard-Jones and coulombic interaction, are they not?

Thank you for your help
Antonia
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Re: [gmx-users] How to handle incomplete PDB file?

[Tsjerk Wassenaar]

Read all mails in this thread... (and the archives)

Tsjerk

On Tue, Mar 3, 2009 at 2:08 PM, Lee Soin  wrote:
> Then what should I do?
>
> 2009/3/3 Justin A. Lemkul 
>>
>>
>> Justin A. Lemkul wrote:
>>
 Specifying -missing in pdb2gmx doesn't work.
>>
>> Also, don't do this.  Note from the pdb2gmx documentation that this is
>> "dangerous."  You will end up with incomplete amino acids, fractional
>> charges, and a completely unrealistic model.
>>
>> -Justin
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> ___
>> gmx-users mailing list    gmx-us...@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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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> Sun Li
> Department of Physics
> Nanjing University, China
>
> ___
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
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] How to handle incomplete PDB file?

[Lee Soin]

Then what should I do?

2009/3/3 Justin A. Lemkul 

>
>
> Justin A. Lemkul wrote:
>
>  Specifying -missing in pdb2gmx doesn't work.
>>>
>>
> Also, don't do this.  Note from the pdb2gmx documentation that this is
> "dangerous."  You will end up with incomplete amino acids, fractional
> charges, and a completely unrealistic model.
>
> -Justin
>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] Can not open file: topol.tpr

[J. Rui Rodrigues]

It's not mdrun -v deffnm em, but:
mdrun -v -deffnm em

Rui




On Tue, 03 Mar 2009 15:52:36 +0300, drugdesign wrote
> Oh, I am very sorry, I've copied the wrong error. Actually error was with the 
> same tutorial at the next step with mdrun -v deffnm em. I can't figure  out 
> why I need topol.tpr for energy minimization? It must be only em.tpr, right? 
> by -v deffnm command?
> 
> ---
> Program mdrun, VERSION 4.0.2
> Source code file: gmxfio.c, line: 736
> 
> Can not open file:
> topol.tpr
> ---
> 
> "I Smell Smoke From a Gun Named Extinction" (Pixies)
> 
> and...@linux-f29d:~/GROMACS_MD/1LYD> mdrun -v deffnm em
> 
>  [UTF-8?]Пересылаемое [UTF-8?]сообщение 
> 02.03.09, 00:19, gmx-users-requ...@gromacs.org:
> 
> Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   gmx-users-requ...@gromacs.org
> 
> You can reach the person managing the list at
>   gmx-users-ow...@gromacs.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
> 
> Today's Topics:
> 
>1. Question (Elias santos)
>2. tool.top does not found (drugdesign)
>3. Re: tool.top does not found (Justin A. Lemkul)
>4. help with FAD topology, please (Miguel Quiliano Meza)
>5. Re: help with FAD topology, please (Justin A. Lemkul)
>6. Re: Question (Mark Abraham)
>7. RE: Cannot obtain the expected pressure using the
>   Parrinello-Rahman coupling in a gas-liquid system (Berk Hess)
> 
> --
> 
> Message: 1
> Date: Sun, 1 Mar 2009 09:14:36 -0300
> From: Elias santos 
> Subject: [gmx-users] Question
> To: gmx-users-request ,gmx-users
>   
> Message-ID:
>   <97baf6380903010414v50f35a14l47d66fbf020a2...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi!!
> 
> I am changing my equipment for a AMD quad Core with two physical
> processors and would like to know if in this configuration I will have
> problems of compatibility with gromacs 4.0.
> 
> Elias Silva
> 
> --
> 
> Message: 2
> Date: Sun, 01 Mar 2009 17:07:25 +0300
> From: drugdesign 
> Subject: [gmx-users] tool.top does not found
> To: gmx-users@gromacs.org
> Message-ID: <29071235916...@webmail45.yandex.ru>
> Content-Type: text/plain; charset=KOI8-R
> 
> Dear GROMACS users,
> I am trying to perform [UTF-8?]thе tutorial listed below with amber03 force 
> field,
>  but I get an error about tool.top while running grompp with em.mdp What can 
> cause such a problem? Best regards, Andrew
> 
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
> 
> This is a command line:
> 
> and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
> solvated.gro -o em.tpr
> 
> checking input for internal consistency...
> 
> ---
> Program grompp, VERSION 4.0.2
> Source code file: grompp.c, line: 810
> 
> Fatal error:
> tool.top does not exist
> ---
> 
> "Baseball Heroes Only" (P.J. Harvey)
> 
> --
> 
> Message: 3
> Date: Sun, 01 Mar 2009 09:54:11 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] tool.top does not found
> To: Discussion list for GROMACS users 
> Message-ID: <49aaa193.4050...@vt.edu>
> Content-Type: text/plain; charset=KOI8-R; format=flowed
> 
> drugdesign wrote:
> > Dear GROMACS users,
> > I am trying to perform [UTF-8?]thе tutorial listed below with amber03 
> > force field, but I get an error
> > about tool.top while running grompp with em.mdp
> > What can cause such a problem?
> > Best regards,
> > Andrew
> > 
> > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 
> > 
> > This is a command line:
> > 
> > and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
> > solvated.gro -o em.tpr
> > 
> > checking input for internal consistency...
> > 
> > ---
> > Program grompp, VERSION 4.0.2
> > Source code file: grompp.c, line: 810
> > 
> > Fatal error:
> > tool.top does not exist
> > ---
> >
> 
> tool.top != topol.top; watch for typos!
> 
> -Justin
> 
> > "Baseball Heroes Only" (P.J. Harvey)
> > 
> > 
> > 
> > ___
> > 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!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to g

Re: [gmx-users] How to handle incomplete PDB file?

[Justin A. Lemkul]

Justin A. Lemkul wrote:


Specifying -missing in pdb2gmx doesn't work.


Also, don't do this.  Note from the pdb2gmx documentation that this is 
"dangerous."  You will end up with incomplete amino acids, fractional charges, 
and a completely unrealistic model.


-Justin

--


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


___
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Re: [gmx-users] How to handle incomplete PDB file?

[Justin A. Lemkul]

Lee Soin wrote:

Hello!
While processing a PDB file, pdb2gmx ended up with the warning

WARNING: atom CG not found in residue 14 while adding atom
 
and the error
 
Fatal error:

Atom CG not found in residue ASP14 while adding hydrogens
 
Specifying -missing in pdb2gmx doesn't work.
 
In the original PDB file, a few missing atoms are listed.
 
What to do in this situation?




Rebuild them with modeling software.

-Justin


--
Sun Li
Department of Physics
Nanjing University, China




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--


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


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Re: [gmx-users] Can not open file: topol.tpr

[Justin A. Lemkul]

drugdesign wrote:

Oh, I am very sorry, I've copied the wrong error. Actually error was with the 
same tutorial at the next step with mdrun -v deffnm em.
I can't figure  out why I need topol.tpr for energy minimization? It must be 
only em.tpr, right? by -v deffnm command?



From the documentation, it might seem that way.  But -deffnm seems to only act 
on output files, so -s is taking the default, topol.tpr.  You need to explicitly 
tell mdrun that your input is em.tpr.


-Justin


---
Program mdrun, VERSION 4.0.2
Source code file: gmxfio.c, line: 736

Can not open file:
topol.tpr
---

"I Smell Smoke From a Gun Named Extinction" (Pixies)

and...@linux-f29d:~/GROMACS_MD/1LYD> mdrun -v deffnm em




 Пересылаемое сообщение 
02.03.09, 00:19, gmx-users-requ...@gromacs.org:

Send gmx-users mailing list submissions to
gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-requ...@gromacs.org

You can reach the person managing the list at
gmx-users-ow...@gromacs.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. Question (Elias santos)
   2. tool.top does not found (drugdesign)
   3. Re: tool.top does not found (Justin A. Lemkul)
   4. help with FAD topology, please (Miguel Quiliano Meza)
   5. Re: help with FAD topology, please (Justin A. Lemkul)
   6. Re: Question (Mark Abraham)
   7. RE: Cannot obtain the expected pressure using the
  Parrinello-Rahman coupling in a gas-liquid system (Berk Hess)


--

Message: 1
Date: Sun, 1 Mar 2009 09:14:36 -0300
From: Elias santos 
Subject: [gmx-users] Question
To: gmx-users-request ,gmx-users

Message-ID:
<97baf6380903010414v50f35a14l47d66fbf020a2...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi!!

I am changing my equipment for a AMD quad Core with two physical
processors and would like to know if in this configuration I will have
problems of compatibility with gromacs 4.0.


Elias Silva


--

Message: 2
Date: Sun, 01 Mar 2009 17:07:25 +0300
From: drugdesign 
Subject: [gmx-users] tool.top does not found
To: gmx-users@gromacs.org
Message-ID: <29071235916...@webmail45.yandex.ru>
Content-Type: text/plain; charset=KOI8-R

Dear GROMACS users,
I am trying to perform thе tutorial listed below with amber03 force field, but 
I get an error
about tool.top while running grompp with em.mdp
What can cause such a problem?
Best regards,
Andrew

https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 


This is a command line:

and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
solvated.gro -o em.tpr

checking input for internal consistency...

---
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 810

Fatal error:
tool.top does not exist
---

"Baseball Heroes Only" (P.J. Harvey)





--

Message: 3
Date: Sun, 01 Mar 2009 09:54:11 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] tool.top does not found
To: Discussion list for GROMACS users 
Message-ID: <49aaa193.4050...@vt.edu>
Content-Type: text/plain; charset=KOI8-R; format=flowed



drugdesign wrote:

Dear GROMACS users,
I am trying to perform thе tutorial listed below with amber03 force field, but 
I get an error
about tool.top while running grompp with em.mdp
What can cause such a problem?
Best regards,
Andrew

https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 


This is a command line:

and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
solvated.gro -o em.tpr

checking input for internal consistency...

---
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 810

Fatal error:
tool.top does not exist
---



tool.top != topol.top; watch for typos!

-Justin


"Baseball Heroes Only" (P.J. Harvey)



___
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!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php





--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]v

[gmx-users] Can not open file: topol.tpr

[drugdesign]

Oh, I am very sorry, I've copied the wrong error. Actually error was with the 
same tutorial at the next step with mdrun -v deffnm em.
I can't figure  out why I need topol.tpr for energy minimization? It must be 
only em.tpr, right? by -v deffnm command?

---
Program mdrun, VERSION 4.0.2
Source code file: gmxfio.c, line: 736

Can not open file:
topol.tpr
---

"I Smell Smoke From a Gun Named Extinction" (Pixies)

and...@linux-f29d:~/GROMACS_MD/1LYD> mdrun -v deffnm em




 Пересылаемое сообщение 
02.03.09, 00:19, gmx-users-requ...@gromacs.org:

Send gmx-users mailing list submissions to
gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-requ...@gromacs.org

You can reach the person managing the list at
gmx-users-ow...@gromacs.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. Question (Elias santos)
   2. tool.top does not found (drugdesign)
   3. Re: tool.top does not found (Justin A. Lemkul)
   4. help with FAD topology, please (Miguel Quiliano Meza)
   5. Re: help with FAD topology, please (Justin A. Lemkul)
   6. Re: Question (Mark Abraham)
   7. RE: Cannot obtain the expected pressure using the
  Parrinello-Rahman coupling in a gas-liquid system (Berk Hess)


--

Message: 1
Date: Sun, 1 Mar 2009 09:14:36 -0300
From: Elias santos 
Subject: [gmx-users] Question
To: gmx-users-request ,  gmx-users

Message-ID:
<97baf6380903010414v50f35a14l47d66fbf020a2...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi!!

I am changing my equipment for a AMD quad Core with two physical
processors and would like to know if in this configuration I will have
problems of compatibility with gromacs 4.0.


Elias Silva


--

Message: 2
Date: Sun, 01 Mar 2009 17:07:25 +0300
From: drugdesign 
Subject: [gmx-users] tool.top does not found
To: gmx-users@gromacs.org
Message-ID: <29071235916...@webmail45.yandex.ru>
Content-Type: text/plain; charset=KOI8-R

Dear GROMACS users,
I am trying to perform thе tutorial listed below with amber03 force field, but 
I get an error
about tool.top while running grompp with em.mdp
What can cause such a problem?
Best regards,
Andrew

https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 

This is a command line:

and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
solvated.gro -o em.tpr

checking input for internal consistency...

---
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 810

Fatal error:
tool.top does not exist
---

"Baseball Heroes Only" (P.J. Harvey)





--

Message: 3
Date: Sun, 01 Mar 2009 09:54:11 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] tool.top does not found
To: Discussion list for GROMACS users 
Message-ID: <49aaa193.4050...@vt.edu>
Content-Type: text/plain; charset=KOI8-R; format=flowed



drugdesign wrote:
> Dear GROMACS users,
> I am trying to perform thе tutorial listed below with amber03 force field, 
> but I get an error
> about tool.top while running grompp with em.mdp
> What can cause such a problem?
> Best regards,
> Andrew
> 
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 
> 
> This is a command line:
> 
> and...@linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
> solvated.gro -o em.tpr
> 
> checking input for internal consistency...
> 
> ---
> Program grompp, VERSION 4.0.2
> Source code file: grompp.c, line: 810
> 
> Fatal error:
> tool.top does not exist
> ---
> 

tool.top != topol.top; watch for typos!

-Justin

> "Baseball Heroes Only" (P.J. Harvey)
> 
> 
> 
> ___
> 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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> 

-- 


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




--

Message: 4
Date: Sun, 1 Mar 2009 11:42:

[gmx-users] How to handle incomplete PDB file?

[Lee Soin]

Hello!
While processing a PDB file, pdb2gmx ended up with the warning

WARNING: atom CG not found in residue 14 while adding atom

and the error

Fatal error:
Atom CG not found in residue ASP14 while adding hydrogens

Specifying -missing in pdb2gmx doesn't work.

In the original PDB file, a few missing atoms are listed.

What to do in this situation?

-- 
Sun Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] regarding dimethylated lysine topology file

[Justin A. Lemkul]

prasun kumar wrote:

Respected all
I drew the structure using the drawing tool available in PRODRG server
then I went for  topology file generation,but the server is deleting 
almost all the hydrogen atoms while writing the topology file for gromacs

can any one tell me why it is doing like this?



Because the PRODRG server is for use with the Gromos force fields, which are 
united-atom.  You can get an all-H structure file as output, but the topology is 
force field-dependent.



another question I got that is
how to change gromacs topology file to charmm topology file
(I know for bond length and anglebut for dihedral(improper and 
proper))


That type of information would be in the Gromacs and CHARMM manuals.

actually i want toi know which function gromacs is using for the 
calculation of dihedrals..


Manual, Chapter 5.

-Justin


thanx in advance

PRASUN (ASHOKA)




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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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] Thank Roland

[mhviet]

Thank Roland very much.
I have read it and I understood it a litle.
Wishing all good things come to you

Man Hoang Viet
>
 Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   gmx-users-requ...@gromacs.org
>
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>   gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. regarding dimethylated lysine topology file (prasun kumar)
>2. Re: How to define protein surface residues (Lee Soin)
>3. about LINCS WARNING (mhv...@ifpan.edu.pl)
>4. Re: about LINCS WARNING (Roland Schulz)
>
>
> --
>
> Message: 1
> Date: Tue, 3 Mar 2009 03:06:17 -0800
> From: prasun kumar 
> Subject: [gmx-users] regarding dimethylated lysine topology file
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Respected all
> I drew the structure using the drawing tool available in PRODRG server
> then I went for  topology file generation,but the server is deleting
> almost
> all the hydrogen atoms while writing the topology file for gromacs
> can any one tell me why it is doing like this?
>
> another question I got that is
> how to change gromacs topology file to charmm topology file
> (I know for bond length and anglebut for dihedral(improper and
> proper))
> actually i want toi know which function gromacs is using for the
> calculation
> of dihedrals..
> thanx in advance
>
> PRASUN (ASHOKA)
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090303/a41dfb5d/attachment-0001.html
>
> --
>
> Message: 2
> Date: Tue, 3 Mar 2009 19:09:20 +0800
> From: Lee Soin 
> Subject: Re: [gmx-users] How to define protein surface residues
> To: Discussion list for GROMACS users 
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks, but what I mean is to just find out the surface residues, not to
> calculate the surface area.
>
> 2009/3/3 David van der Spoel 
>
>> Lee Soin wrote:
>>
>>> Hello!
>>> I'm trying to find the surface residues of a protein. Maybe this should
>>> be
>>> calculated by myself and not using GROMACS. Can anybody tell me a
>>> feasible
>>> procedure for doing so? Thanks!
>>>
>> g_sas
>>
>>  --
>>> Sun Li
>>> Department of Physics
>>> Nanjing University, China
>>>
>>>
>>> 
>>>
>>> ___
>>> 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!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface
>> or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Sun Li
> Department of Physics
> Nanjing University, China
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090303/4ddc0177/attachment-0001.html
>
> --
>
> Message: 3
> Date: Tue, 3 Mar 20

Re: [gmx-users] about LINCS WARNING

[Roland Schulz]

Are you sure you are actually doing minimization and not MD? Check the
integrator option in the mdp file. Also take a look at:
http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

Roland

On Tue, Mar 3, 2009 at 6:19 AM,  wrote:

> Thank David very much
> I have tried and most of them work.
> And, When I run script_mini.mdp to minimize energy and it report LINCS
> warning (as below). So Can you tell me What LINCS WARNING mean?
>
> Step 16, time 0.032 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.00, max 0.01 (between atoms 18 and 20)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 97 98   35.30.1000   0.1000  0.1000
>
>
>
> > Send gmx-users mailing list submissions to
> >   gmx-users@gromacs.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >   http://www.gromacs.org/mailman/listinfo/gmx-users
> > or, via email, send a message with subject or body 'help' to
> >   gmx-users-requ...@gromacs.org
> >
> > You can reach the person managing the list at
> >   gmx-users-ow...@gromacs.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. Detail of Script.sh in Gromacs-4.0.3? (mhv...@ifpan.edu.pl)
> >2. Re: How to define protein surface residues (David van der Spoel)
> >3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel)
> >4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke)
> >
> >
> > --
> >
> > Message: 1
> > Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET)
> > From: mhv...@ifpan.edu.pl
> > Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
> > To: gmx-users@gromacs.org
> > Message-ID:
> >   <24e6018b503b7a1516fccea3477b4d8d.squir...@webmail.ifpan.edu.pl>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Dear all
> >
> > I am newer in Gromacs. Now I am studying Gomacs for protein simulations.
> I
> > am trying script files which used for gromacs-3. Can I do it? Does
> > Gromacs-4. have to use others script files? and If It have, Can you send
> > sript files to me for gromacs-4?
> > Thank you verry much!
> >
> > Yours truly,
> >
> > Man Hoang Viet
> >
> >
> >
> > --
> >
> > Message: 2
> > Date: Tue, 03 Mar 2009 10:52:07 +0100
> > From: David van der Spoel 
> > Subject: Re: [gmx-users] How to define protein surface residues
> > To: Discussion list for GROMACS users 
> > Message-ID: <49acfdc7.6060...@xray.bmc.uu.se>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Lee Soin wrote:
> >> Hello!
> >> I'm trying to find the surface residues of a protein. Maybe this should
> >> be calculated by myself and not using GROMACS. Can anybody tell me a
> >> feasible procedure for doing so? Thanks!
> >>
> > g_sas
> >
> >> --
> >> Sun Li
> >> Department of Physics
> >> Nanjing University, China
> >>
> >>
> >> 
> >>
> >> ___
> >> 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!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
> +4618511755.
> > sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
> >
> >
> > --
> >
> > Message: 3
> > Date: Tue, 03 Mar 2009 10:54:42 +0100
> > From: David van der Spoel 
> > Subject: Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
> > To: Discussion list for GROMACS users 
> > Message-ID: <49acfe62.6030...@xray.bmc.uu.se>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > mhv...@ifpan.edu.pl wrote:
> >> Dear all
> >>
> >> I am newer in Gromacs. Now I am studying Gomacs for protein simulations.
> >> I
> >> am trying script files which used for gromacs-3. Can I do it? Does
> >> Gromacs-4. have to use others script files? and If It have, Can you send
> >> sript files to me for gromacs-4?
> >> Thank you verry much!
> >
> > Have you tried?
> >
> > Most of them will work.
> >
> >>
> >> Yours truly,
> >>
> >> Man Hoang Viet
> >>
> >> ___
> >> 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!
> >> Please don't post 

[gmx-users] about LINCS WARNING

[mhviet]

Thank David very much
I have tried and most of them work.
And, When I run script_mini.mdp to minimize energy and it report LINCS
warning (as below). So Can you tell me What LINCS WARNING mean?

Step 16, time 0.032 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.01 (between atoms 18 and 20)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 97 98   35.30.1000   0.1000  0.1000



> Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>   gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Detail of Script.sh in Gromacs-4.0.3? (mhv...@ifpan.edu.pl)
>2. Re: How to define protein surface residues (David van der Spoel)
>3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel)
>4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke)
>
>
> --
>
> Message: 1
> Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET)
> From: mhv...@ifpan.edu.pl
> Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
> To: gmx-users@gromacs.org
> Message-ID:
>   <24e6018b503b7a1516fccea3477b4d8d.squir...@webmail.ifpan.edu.pl>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear all
>
> I am newer in Gromacs. Now I am studying Gomacs for protein simulations. I
> am trying script files which used for gromacs-3. Can I do it? Does
> Gromacs-4. have to use others script files? and If It have, Can you send
> sript files to me for gromacs-4?
> Thank you verry much!
>
> Yours truly,
>
> Man Hoang Viet
>
>
>
> --
>
> Message: 2
> Date: Tue, 03 Mar 2009 10:52:07 +0100
> From: David van der Spoel 
> Subject: Re: [gmx-users] How to define protein surface residues
> To: Discussion list for GROMACS users 
> Message-ID: <49acfdc7.6060...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Lee Soin wrote:
>> Hello!
>> I'm trying to find the surface residues of a protein. Maybe this should
>> be calculated by myself and not using GROMACS. Can anybody tell me a
>> feasible procedure for doing so? Thanks!
>>
> g_sas
>
>> --
>> Sun Li
>> Department of Physics
>> Nanjing University, China
>>
>>
>> 
>>
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
>
>
> --
>
> Message: 3
> Date: Tue, 03 Mar 2009 10:54:42 +0100
> From: David van der Spoel 
> Subject: Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?
> To: Discussion list for GROMACS users 
> Message-ID: <49acfe62.6030...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> mhv...@ifpan.edu.pl wrote:
>> Dear all
>>
>> I am newer in Gromacs. Now I am studying Gomacs for protein simulations.
>> I
>> am trying script files which used for gromacs-3. Can I do it? Does
>> Gromacs-4. have to use others script files? and If It have, Can you send
>> sript files to me for gromacs-4?
>> Thank you verry much!
>
> Have you tried?
>
> Most of them will work.
>
>>
>> Yours truly,
>>
>> Man Hoang Viet
>>
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
>
>
> --
>
> Message: 4
> Date: Tue, 3 Mar 2

Re: [gmx-users] How to define protein surface residues

[Lee Soin]

Thanks, but what I mean is to just find out the surface residues, not to
calculate the surface area.

2009/3/3 David van der Spoel 

> Lee Soin wrote:
>
>> Hello!
>> I'm trying to find the surface residues of a protein. Maybe this should be
>> calculated by myself and not using GROMACS. Can anybody tell me a feasible
>> procedure for doing so? Thanks!
>>
> g_sas
>
>  --
>> Sun Li
>> Department of Physics
>> Nanjing University, China
>>
>>
>> 
>>
>> ___
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
> ___
> 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!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Sun Li
Department of Physics
Nanjing University, China
___
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] regarding dimethylated lysine topology file

[prasun kumar]

Respected all
I drew the structure using the drawing tool available in PRODRG server
then I went for  topology file generation,but the server is deleting almost
all the hydrogen atoms while writing the topology file for gromacs
can any one tell me why it is doing like this?

another question I got that is
how to change gromacs topology file to charmm topology file
(I know for bond length and anglebut for dihedral(improper and
proper))
actually i want toi know which function gromacs is using for the calculation
of dihedrals..
thanx in advance

PRASUN (ASHOKA)
___
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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www interface or send it to gmx-users-requ...@gromacs.org.
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SV: SV: [gmx-users] g_order version 4.0.x

[Sarah Witzke]

Good idea, I'll try that when I get home next week.
 
-Sarah



Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul
Sendt: ma 02-03-2009 13:58
Til: Discussion list for GROMACS users
Emne: Re: SV: [gmx-users] g_order version 4.0.x





Sarah Witzke wrote:
> Thank you David, I have filled a bugzilla.
>

g_order works for me under version 4.0.4, perhaps try an upgrade?

-Justin

  
>
> Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel
> Sendt: ma 02-03-2009 10:55
> Til: Discussion list for GROMACS users
> Emne: Re: [gmx-users] g_order version 4.0.x
>
>
>
> Sarah Witzke wrote:
>> Dear Gromacs users,
>>
>>
>>
>> I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I 
>> still haven't received it myself. I'm sorry for the inconvenience it might 
>> cause.
>>
>>
>>
>> Sarah
>>
>>
>> 
>>
>> Dear Gromacs Users,
>>
>>
>>
>> I have simulated a lipid bilayer (128 DMPC molecules) with some small 
>> hydrophobic molecules. These small molecules go from the water into the 
>> bilayer and I now want to do some analysis to see, whether this has changed 
>> e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs 
>> and this is my first try with analysis.
>>
>> For analysing the order of the lipid tales, I use g_order. The first index 
>> file I created consisted of 28 groups - one for each of the 14 carbons 
>> (including the carbonyl-C) in the two chains. The atoms in each of the 128 
>> lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 
>> groups in the index file consist of 128 atoms (an entry in make_ndx would 
>> look like this "a c15 & r DMPC").
>>
>> Then I tried g_order version 4.0.2:
>>
>>
>>
>> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 
>> -od dmpclim3_order_2.xvg
>>
>>
>>
>> I'm asked to "Select the group that contains the atoms you want to use for 
>> the tetrahedrality order parameter calculation:" and then all the 28 groups 
>> are listed. This was not what I had expected; I thought g_order calculated 
>> the order parameter for all the tail carbons at once. I tried just choosing 
>> group 0 to see what happened: Not much - as was expected. Two files were 
>> generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't 
>> asked for them, but then I found this bugzilla report: 
>> http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ 
>> 
>>   (no. 264)
>>
>>
>>
>>
>>
>> After reading that I also tried to specify all carbons in one single group 
>> and then run g_order again:
>>
>>
>>
>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 
>> -od dmpclim3_order_2.xvg
>>
>>
>>
>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>>
>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>>
>> Select the group that contains the atoms you want to use for the 
>> tetrahedrality order parameter calculation:
>>
>> Group 0 
>> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC)
>>  has  3584 elements
>>
>> There is one group in the index
>>
>> Reading frame   0 time 10.008
>>
>> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#
>>
>>
>>
>> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
>>
>> Reading frame   11000 time 21.016
>>
>>
>>
>> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted deuterium 
>> order .xvg file.
>>
>>
>>
>> So, in the bugzilla report it also said that the problem had been fixed in 
>> the CVS. Unfortunately I don't know what this is, could anyone explain me 
>> please?
>>
>>
>>
>> I tried g_order version 4.0.3 (again with the index file with only one 
>> group):
>>
>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 
>> -od dmpclim3_order_3.xvg
>>
>>
>>
>> Taking z axis as normal to the membrane
>>
>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision)
>>
>> Using following groups:
>>
>> Groupname: 
>> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC
>>  First atomname: C15 First atomnr 44
>>
>>
>>
>> Reading frame   0 time 10.008   Number of elements in first group: 
>> 3584
>>
>> Reading frame   11000 time 21.016
>>
>>
>>
>> Read trajectory. Printing parameters to file
>>
>>
>>
>> Now two order file

Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3?

[David van der Spoel]

mhv...@ifpan.edu.pl wrote:

Dear all

I am newer in Gromacs. Now I am studying Gomacs for protein simulations. I
am trying script files which used for gromacs-3. Can I do it? Does
Gromacs-4. have to use others script files? and If It have, Can you send
sript files to me for gromacs-4?
Thank you verry much!


Have you tried?

Most of them will work.



Yours truly,

Man Hoang Viet

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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] How to define protein surface residues

[David van der Spoel]

Lee Soin wrote:

Hello!
I'm trying to find the surface residues of a protein. Maybe this should 
be calculated by myself and not using GROMACS. Can anybody tell me a 
feasible procedure for doing so? Thanks! 


g_sas


--
Sun Li
Department of Physics
Nanjing University, China




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] Detail of Script.sh in Gromacs-4.0.3?

[mhviet]

Dear all

I am newer in Gromacs. Now I am studying Gomacs for protein simulations. I
am trying script files which used for gromacs-3. Can I do it? Does
Gromacs-4. have to use others script files? and If It have, Can you send
sript files to me for gromacs-4?
Thank you verry much!

Yours truly,

Man Hoang Viet

___
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[gmx-users] How to define protein surface residues

[Lee Soin]

Hello!
I'm trying to find the surface residues of a protein. Maybe this should be
calculated by myself and not using GROMACS. Can anybody tell me a feasible
procedure for doing so? Thanks!

-- 
Sun Li
Department of Physics
Nanjing University, China
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