Re: [gmx-users] Need Help on Simulated annealing (Implicit Solvation)

[Justin Lemkul]

On 1/24/13 10:26 AM, Raghuvir R. S. Pissurlenkar wrote:

Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide 
(~30 aa) in implicit solvent.

Please someone could tell me if the parameters set are fine for the same.

-
; Preprocessing
define = -DFLEXIBLE



Irrelevant if there is no explicit water, and shouldn't be used for MD anyway 
(only EM).



; Run control
integrator = md
dt = 0.002
nsteps = 50; 1 ns
comm-mode = angular
nstcomm = 1000


grompp will complain about this.  nstcomm should be equal to nstcalcenergy.


comm-grps = system

; Langevin dynamics
bd-fric = 0
ld-seed = 1993

; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000

; Neighbor searching
cutoff-scheme = group
nstlist = 10


Better to use a fixed neighbor list (nstlist = 0) to use the all-vs-all kernels. 
 You're using infinite cutoffs anyway, so all interactions are calculated. 
There's no point in updating a neighbor list that contains every atom in it.



ns-type = simple
pbc = no
rlist = 0

; Electrostatics
coulombtype = cut-off
rcoulomb = 0

; VdW
vdwtype = cut-off
rvdw = 0

; Temperature coupling
tcoupl = v-rescale
tc-grps = Protein
tau-t = 0.5
ref-t = 300.0

; Pressure coupling
pcoupl = no

; Simulated annealing
annealing = single
annealing-npoints = 1
annealing-npoints = 0 10 20 30 40 50


You've got the same keyword twice.  The first instance (annealing-npoints = 1) 
is correct; there is only one group specified in tc-grps.


Presumably what you want here is annealing-time rather than annealing-npoints.


annealing-temp = 300 320 340 360 380 400



Simulated annealing is a linear increase in temperature, and thus all you need 
to do to warm from 300K to 400K over 50 ps is:


annealing-time = 0 50
annealing-temp = 300 400


; Velocity generation
gen-vel = yes
gen-temp = 300.0
gen-seed = 173529

; Bonds
constraints = all-bonds
constraint-algorithm = P-LINCS


P-LINCS is not a valid setting.  If running in parallel, LINCS automatically 
uses P-LINCS.



lincs-order = 4
lincs-iter = 1

; Implicit solvent
implicit-solvent = GBSA
gb-algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0


Set both nstgbradii and rgbradii to zero when using infinite cutoffs.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Need help with tabulated non-bonding potential tablep file

[Justin A. Lemkul]

On 4/23/12 8:54 AM, Marcelo Lopez wrote:

I get no answer so I insist... ¿Do my questions gets in to the email list?



Your messages are arriving on the list.  The documentation for tablep.xvg 
contents is certainly lacking, and unfortunately so too are the threads in the 
archive on the same topic.  Most of them are unanswered or incomplete and thus, 
if you are receiving no reply, we don't know how to offer complete help.


You may have to dive into the code to see how these files are read and utilized. 
 It's not small task, but you'll certainly get your questions answered :)


-Justin


Hi all: I'm trying to run a coarse grained system with 3 different
kind of particles, lets call them "A", "B" and "C", and the
interactions between them are set by means of 3 tabulated potentials
(not LJ, totally customized ones). I want to introduce 1-4
interactions with the -tablep optional argument of mdrun. I don't
understand:

1) How exactly to write one tablep.xvg file? 3 or 4 values for each
pair? For example, for the atom indexes 1 and 5, must I write

1   5   0.0   0.0
or
150.0
?

Or must I write the atom labels?:

AB0.0   0.0

2) Must I put only one tablep.xvg file with all the pairs or must I
make one separated table for each kind of 1-4 interaction? For
example:

tablep.xvg (with all the interactions)

or

tablep.xvg, tablep_A_A.xvg, tablep_B_B.xvg, tablep_A_C.xvg, ..

3) mdrun expects the indexes and 1 or 2 values?

4) What's the meaning of the value/s at the right of the 2 indexes for
a not LJ tabulated potential?

5) The pair interactions are scaled or set to zero when using
tabulated non-bonding potentials? I need to set them zero...

Thank you in advance.

Johny.


--


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


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Re: [gmx-users] need help with topology file

[Justin A. Lemkul]

jampani srinivas wrote:

Hi,

I am trying to use two types of force fields for my system which has 
protein and fullerene. i want to use OPLS for protein and ffG53a6 for 
fullerene(as i don't have opls readily available for this). When i use 
two itp files in #include section grompp does not allow me to do that 
with the following error. 
---

Program grompp, VERSION 4.0.5
Source code file: topio.c, line: 430

Fatal error:
Syntax error - File ffG53a6.itp, line 6
Last line read:
'  1 1 no 1.0 1.0'
Found a second defaults directive.

---

Chapter 5 in manual has information about using topology files but i am 
not clear about using #define. Can anybody help me how to use opls for 
protein and gromos for fullerene in the same system? 



That will be a meaningless combination.  The force fields use completely 
different combination rules (and hence why you're getting the fatal error about 
trying to use two different [defaults] sections) and are based on different 
parameterization strategies.  You need a self-consistent model and any attempt 
to combine force fields in this way will not succeed.


-Justin

--


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


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Re: [gmx-users] need help

[Mark Abraham]

On 23/05/2011 6:57 PM, rashi parihar wrote:


Hi all
I have an ligand having NI atom(Nickel) .Now problem is this when I am 
running PRODRG server ,ligand topology can not be created and error is 
coming

*unsupported atom type NI (atom 'NI2 ') in your coordinates*.now how to 
overcome this problem? plz help me!!


See http://www.gromacs.org/Documentation/How-tos/Parameterization

Mark
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Re: [gmx-users] Need help troubleshooting an mdrun-gpu error message!

[Szilárd Páll]

Hi,

There are two things you should test:

a) Does your NVIDIA driver + CUDA setup work? Try to run a different
CUDA-based program, e.g. you can get the CUDA SDK and compile one of
the simple programs like deviceQuery or bandwidthTest.

b) If the above works, try to compile OpenMM from source with the same
CUDA version as the one used when compiling Gromacs.

Let me know if you succeed!

Cheers,
--
Szilárd



On Tue, Jan 25, 2011 at 3:49 AM, Solomon Berman  wrote:
> Hello friends,
> I have installed mdrun-gpu v. 4.5.3 without incident on my group's computer
> with a suitable GPU.  The computer uses a Linux OS.  CUDA and OpenMM are
> installed in the usual places.  I created the topol.tpr file with grompp v.
> 4.5.3, also without incident.  When I run ./mdrun-gpu -v, the following
> error message is produced:
> Program mdrun-gpu, VERSION 4.5.3
> Source code file:
> /home/smberman/sourcecode/gromacs-4.5.3/src/kernel/openmm_wrapper.cpp, line:
> 1259
> Fatal error:
> The requested platform "CUDA" could not be found.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> I have the following in my .bash_profile:
> export PATH=~/bin:~/usr/bin:~/usr/local/bin:/usr/local/cuda/bin:$PATH:.
> LD_LIBRARY_PATH="/usr/local/openmm/lib:/usr/local/cuda/lib"
> export LD_LIBRARY_PATH
> I have run the available tests that came with the OpenMM library, and the
> CUDA tests pass.
> Could someone please explain what this error means and the appropriate way
> to remedy it?  Thank you!!
> Best,
> Solomon Berman
> Chemistry Department
> Boston University
>
> --
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Re: [gmx-users] Need help!!!

[Justin A. Lemkul]

#ZHAO LINA# wrote:

But it's a bit trivial to modify those things if you just following those steps 
by steps.
Using the latest version can save lots of works.



Indeed.  But I'm also a fan of solving one problem at a time.  A broken force 
field file won't get fixed by trying to simultaneously accommodate a new 
organization and understand the intrinsics of Gromacs.



By the way, thanks for the website, I once followed that too (nearly step by 
step also).



Glad it was useful.  When you say "nearly," were there parts that didn't make 
sense/didn't work?



Thanks with best regards,

lina

P.S actually you can upgrade your website also. ^_^ 


I realize that.  But I do not have the time to do it, nor will I anytime in the 
near future.  I've got a system that works, and if users are comfortable enough 
with the tutorial as is, then (as you say) it should be easy to convert over to 
the new system.  For anyone new to the game, it may be useful to do the tutorial 
as is, learn Gromacs a bit more thoroughly, then undertake an adventure :)


-Justin



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, September 02, 2010 9:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Need help!!!

#ZHAO LINA# wrote:

Make sure your gromacs is the latest version.
If not, update and try again.



The tutorial is specifically written for version 4.0.5, but will be compatible
with any version <4.5.  Since the re-organization of the force field
directories, the information provided in the tutorial is not correct.

I would recommend not upgrading until the OP has sorted out the problem and can
then (maybe) work out the appropriate translation to the version 4.5.x scheme.

-Justin



*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of praba vathy [sumipraba2...@gmail.com]
*Sent:* Thursday, September 02, 2010 9:06 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Need help!!!

Hi,

I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).

We have used the commands and steps as described in the above link.
But we have got a fatal error (Atom type C not found) while running this
command,

grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp <http://em.tp>

I cant sort out this problem.
Please anybody help me to sort out this problem.
Awaiting for your valuable replies.

Praba



--


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


--
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--


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


--
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RE: [gmx-users] Need help!!!

[#ZHAO LINA#]

But it's a bit trivial to modify those things if you just following those steps 
by steps.
Using the latest version can save lots of works.

By the way, thanks for the website, I once followed that too (nearly step by 
step also).

Thanks with best regards,

lina

P.S actually you can upgrade your website also. ^_^ 

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, September 02, 2010 9:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Need help!!!

#ZHAO LINA# wrote:
> Make sure your gromacs is the latest version.
> If not, update and try again.
>

The tutorial is specifically written for version 4.0.5, but will be compatible
with any version <4.5.  Since the re-organization of the force field
directories, the information provided in the tutorial is not correct.

I would recommend not upgrading until the OP has sorted out the problem and can
then (maybe) work out the appropriate translation to the version 4.5.x scheme.

-Justin

>
> 
> *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of praba vathy [sumipraba2...@gmail.com]
> *Sent:* Thursday, September 02, 2010 9:06 PM
> *To:* gmx-users@gromacs.org
> *Subject:* [gmx-users] Need help!!!
>
> Hi,
>
> I am using simulation for a membrane protein.
> So i have downloaded the dppc.pdb along with it's topology files.
> I have used the following steps for the simulation (Based on the link:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).
>
> We have used the commands and steps as described in the above link.
> But we have got a fatal error (Atom type C not found) while running this
> command,
>
> grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp <http://em.tp>
>
> I cant sort out this problem.
> Please anybody help me to sort out this problem.
> Awaiting for your valuable replies.
>
> Praba
>

--


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


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Re: [gmx-users] Need help!!!

[Justin A. Lemkul]

#ZHAO LINA# wrote:

Make sure your gromacs is the latest version.
If not, update and try again.



The tutorial is specifically written for version 4.0.5, but will be compatible 
with any version <4.5.  Since the re-organization of the force field 
directories, the information provided in the tutorial is not correct.


I would recommend not upgrading until the OP has sorted out the problem and can 
then (maybe) work out the appropriate translation to the version 4.5.x scheme.


-Justin

 

*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
behalf of praba vathy [sumipraba2...@gmail.com]

*Sent:* Thursday, September 02, 2010 9:06 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Need help!!!

Hi,

I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).

We have used the commands and steps as described in the above link.
But we have got a fatal error (Atom type C not found) while running this 
command,


grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp 

I cant sort out this problem.
Please anybody help me to sort out this problem.
Awaiting for your valuable replies.

Praba



--


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


--
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Re: [gmx-users] Need help!!!

[Justin A. Lemkul]

praba vathy wrote:

Hi,

I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).

We have used the commands and steps as described in the above link.
But we have got a fatal error (Atom type C not found) while running this 
command,


grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp 

I cant sort out this problem.
Please anybody help me to sort out this problem.
Awaiting for your valuable replies.



This is a very different error than what you reported before, and since dppc.itp 
does not contain atom type "C" the error indicates (once again) that you have 
incorrectly constructed the ffG53a6nb_lipid.itp file that is described in the 
tutorial.  Please start over and follow the instructions closely.  If you do so, 
you will not get errors about missing atom types.


-Justin


Praba



--


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


--
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RE: [gmx-users] Need help!!!

[#ZHAO LINA#]

Make sure your gromacs is the latest version.
If not, update and try again.



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of praba vathy [sumipraba2...@gmail.com]
Sent: Thursday, September 02, 2010 9:06 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Need help!!!

Hi,

I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).

We have used the commands and steps as described in the above link.
But we have got a fatal error (Atom type C not found) while running this 
command,

grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp

I cant sort out this problem.
Please anybody help me to sort out this problem.
Awaiting for your valuable replies.

Praba
-- 
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Re: [gmx-users] need help

[Mark Abraham]

- Original Message -
From: Anamika Awasthi 
Date: Thursday, August 12, 2010 16:41
Subject: [gmx-users] need help
To: gmx-users@gromacs.org

> Dear gromacs user,
> 
>   I want to install gromacs new version on my linux system. can u all please 
> guide me,

The GROMACS installation guide can be found on the GROMACS webpage :-) There's 
a ton of other useful information there, please be sure to search it and the 
rest of the web before asking questions. You'll make much faster progress that 
way! :-)

Mark

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Re: [gmx-users] Need help with installation on Itanium2

[Vasilii Artyukhov]

Yep, my mistake, I built the serial version using gcc previously, so the
problem really _is_ in Intel's compiler. I've finally figured out how to
make mpicc use gcc instead of Intel, so now I have a working MPI version of
GROMACS.

Thank you again,
Vasilii

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>:

>
> I get the same issue with GROMACS 3.3.2 and 3.3.3 on my Itanium2 system
> using Intel 10.1 icc, and I also get them even without --enable-mpi, e.g.
>
> ../configure --program-suffix=_3.3.3_single --with-fft=fftw2
> --with-external-blas --with-external-lapack
> LIBS="-L/opt/fftw-2.1.5/intel-9.1/lib -lscs"
>
> then make gives
>
> /bin/sh ../../../../libtool   --mode=compile icc -DHAVE_CONFIG_H -I.
> -I../../../../src
> -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single
> -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -w
> -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF
> .deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo
> ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S
>  icc -DHAVE_CONFIG_H -I. -I../../../../src
> -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single
> -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -w
> -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF
> .deps/nb_kernel010_ia64_single.Tpo -c
> ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S
> -o nb_kernel010_ia64_single.o
> /tmp/iccEJOKXd.s(1) : error A2040: Unexpected token: Unary Diez Operator
> at: Start
> ...etc
>
> Running the above icc by hand with -O0 also fails in the same way.
>
>
> Mark
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Re: [gmx-users] Need help with installation on Itanium2

[Mark Abraham]

Vasilii Artyukhov wrote:

Thanks for quick reply,

2008/4/28 Mark Abraham <[EMAIL PROTECTED] 
>:


Vasilii Artyukhov wrote:

Dear everyone,

I'm trying to install GROMACS on an Itanium2 cluster using MPI
icc. At a certain point, the compilation crashes with


What hardware, compilers, GROMACS version and configure command line
were you using?


GROMACS 3.3.3, Itanium2, Intel cc version 9.0, MPICH-GM comm lib. As for 
configure, nothing interesting, just --disable-nice --enable-mpi CC=icc 
& the libs; the serial version (same without --enable-mpi) installs 
successfully, so I kind of hope it's only a problem of assembly loops & 
Intel's cc.


I get the same issue with GROMACS 3.3.2 and 3.3.3 on my Itanium2 system 
using Intel 10.1 icc, and I also get them even without --enable-mpi, e.g.


../configure --program-suffix=_3.3.3_single --with-fft=fftw2 
--with-external-blas --with-external-lapack 
LIBS="-L/opt/fftw-2.1.5/intel-9.1/lib -lscs"


then make gives

/bin/sh ../../../../libtool   --mode=compile icc -DHAVE_CONFIG_H -I. 
-I../../../../src 
-I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single 
-I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-O3 -w -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF 
.deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo 
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S
 icc -DHAVE_CONFIG_H -I. -I../../../../src 
-I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single 
-I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-O3 -w -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF 
.deps/nb_kernel010_ia64_single.Tpo -c 
../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S 
-o nb_kernel010_ia64_single.o
/tmp/iccEJOKXd.s(1) : error A2040: Unexpected token: Unary Diez Operator 
at: Start

...etc

Running the above icc by hand with -O0 also fails in the same way.

Mark
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Re: [gmx-users] Need help with installation on Itanium2

[Vasilii Artyukhov]

Thanks for quick reply,

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>:

> Vasilii Artyukhov wrote:
>
> > Dear everyone,
> >
> > I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a
> > certain point, the compilation crashes with
> >
>
> What hardware, compilers, GROMACS version and configure command line were
> you using?


GROMACS 3.3.3, Itanium2, Intel cc version 9.0, MPICH-GM comm lib. As for
configure, nothing interesting, just --disable-nice --enable-mpi CC=icc &
the libs; the serial version (same without --enable-mpi) installs
successfully, so I kind of hope it's only a problem of assembly loops &
Intel's cc.


>
>
> Mark
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Re: [gmx-users] Need help with installation on Itanium2

[Mark Abraham]

Vasilii Artyukhov wrote:

Dear everyone,

I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a 
certain point, the compilation crashes with


What hardware, compilers, GROMACS version and configure command line 
were you using?


Mark
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Re: [gmx-users] Need help: error during installation

[David van der Spoel]

shyamala iyer wrote:

Hi,
 
I am new to GROMACS and I am having some trouble installing GROMACS in 
my home directory.
The machine I am currently working on has fftw, gcc and binutils already 
installed

fftw package installed: fftw3-3.0.1-4

gcc:
gcc-c++-3.4.6-3.1
libgcc-3.4.6-3.1
compat-libgcc-296-2.96-132.7.2
gcc-3.4.6-3.1
gcc-java-3.4.6-3.1
libgcc-3.4.6-3.1
gcc-g77-3.4.6-3.1

Binutils package:

binutils-2.15.92.0.2-21

After extracting the gromacs-3.3.1 , I followed instructions, went to 
the gromacs dir and typed ./configure with prefix option so that I could 
install GROMACS in my home dir. This fails with the following message:

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for C compiler default output file name... configure: error: C 
compiler cannot create executables

See `config.log' for more details.
 
The location in config.log where I think it is failing is

gcc version 3.4.6 20060404 (Red Hat 3.4.6-3)
configure:2721: $? = 0
configure:2723: gcc -V &5
gcc: `-V' option must have argument
configure:2726: $? = 1
configure:2749: checking for C compiler default output file name
configure:2752: gcc -O3 -Wall -pedantic -static $(HDRS) $(DEFINES)   
conftest.c\

 -lm >&5
gcc: $(HDRS): No such file or directory
gcc: $(DEFINES): No such file or directory
configure:2755: $? = 1
configure: failed program was:
| /* confdefs.h.  */
 
Does someone have any suggestions that I could follow to try and fix 
this error.
 
Thanks a lot,
 
Shyamala



are you sure gcc is in your path? try
gcc -v

can you post the few lines following the config.log snippet that you 
included.


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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