Re: [gmx-users] Acpype Parameter Error?

[Alan]

I will have a look coming Monday. Thanks for reporting that.

Alan

On 24 February 2012 23:25, Kyle Greenway  wrote:

>
> Hello,
>
> This email is directed mainly to Alan, who created Acpype.
>
> I've noticed that Acpype has assigned dihedral constants as 0.65084 for
> many dihedrals of the form X -c3-n4-X, X -c3-c3-X, and others, in my
> generated GROMACS .itp files.  These dihedrals have values of 1.400 in the
> amber 99sb .dat file, which should have instead given 1.4*4.184 = 5.858 for
> the result.
>
> Most other dihedrals I've checked have behaved normally and their values
> correspond to what would be expected - except for dihedrals with values of
> 0.65084 in the .itp files.
>
> Any ideas about what's going on?
>
> Thanks for your time.
>
> Kyle Greenway
>
>
>
>
>
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Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
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[gmx-users] rerun problem

[ahmet yıldırım]

Dear users,

I am using Gromacs 4.5.4. I rerun the simulation using the following
command:
mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append
Unfortunately remaining output didnt append to existing files
(protein-RUN.xtc, protein-RUN.edr,
protein-RUN.log). On the contrary remaining output appended to new files
(traj.xtc, ener.edr, md.log).

What should I do?

Cheers,

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Re: [gmx-users] Positive Coul. recip. term

[Dommert Florian]

On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote:
> Thank you both for your replies.  I currently have another ionic
> liquid running just fine on the same gromacs build (compiled the tpr
> file yesterday), so I am reluctant to conclude that the problem is
> with the linking.  Please let me know if you disagree.  
> The force field I am using was published in 2004 and has been
> validated by another group.  I have double and triple checked my itp
> files to make sure they match the force field, but it's possible there
> are still some errors there. 

Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who
validated it, I am just curious, and what is the ionic liquid ? 

Though you are constraining the hbonds, I would be cautious with the
time step of 2fs, because it might be, that the eigenfrequency of the
anionic bonds requires a shorter time step, but this should not be the
problem of a positive Coulomb energy. Have you calculated the error in
the electrostatic force ? I would suggest to tune it to a limit of 1e-3,
perhaps this resolves the problem of the positive Coulomb term.

Perhaps some 1--4 and dihedral interactions are missing in the itp file,
so assure if all of them are provided correctly.

/Flo

> I agree that this is very strange and feel that there must be
> something fundamentally wrong in the mdp file or deeper.  I have
> included my mdp file below.
> 
> 
> title   =  PMP+TFN
> cpp =  /lib/cpp
> constraints =  hbonds
> integrator  =  md
> dt  =  0.002   ; ps !
> nsteps  =  1000   ; total 20 ns
> nstcomm =  10
> nstxout =  5
> nstvout =  5
> nstfout =  0
> nstlog  =  5000
> nstenergy   =  5000
> nstxtcout   =  25000
> nstlist =  10
> ns_type =  grid
> pbc =  xyz
> coulombtype =  PME
> vdwtype =  Cut-off
> rlist   =  1.2
> rcoulomb=  1.2
> rvdw=  1.2
> fourierspacing  =  0.12
> pme_order   =  4
> ewald_rtol  =  1e-5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl  =  v-rescale
> tc_grps =  PMP   TFN 
> tau_t   =  0.2  0.2 
> ref_t   =  300  300
> nsttcouple  =  1
> ; Energy monitoring
> energygrps  =  PMP   TFN
> ; Isotropic pressure coupling is now on
> Pcoupl  =  berendsen
> pcoupltype  =  isotropic
> tau_p   =  2.0
> ref_p   =  1.0
> compressibility =  4.5e-5
> 
> 
> ; Generate velocites is on at 300 K.
> gen_vel =  yes
> gen_temp=  300.0
> gen_seed=  -1
> 
> 
> 
> On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian
>  wrote:
> On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:
> > Dear all,
> > I am trying to equilibrate a solvent of pure ionic liquid.
>  The system
> > keeps exploding (after 2-5 ns) and I am not sure why, though
> I believe
> > coulombic interactions are to blame.  This is because the
> Coul-SR term
> > is negative, but the Coul. recip term is very positive
> throughout the
> > entire run (giving the entire system a positive potential
> energy).  I
> > think this means that the short-range electrostatics are
> okay, but the
> > long range electrostatics (calculated with PME) are not.
>  Does anybody
> > have any suggestions as to why this would happen?  I have
> used the
> > exact same PME input parameters for another ionic liquid
> that works
> > just fine.  They are listed below.
> >
> >
> > rcoulomb = 1.2
> > fourierspacing = 0.12
> > pme_order = 4
> > ewald_rtol = 1e-5
> >
> 
> 
> Depends on the force field you are using. Perhaps it ist not
> validated
> for the ionic liquid you want to study. It is especially
> strange, that
> it takes so long for your system to blow up.
> 
> Moreoever I would try to optimize the PME settings with the
> tools,
> g_tune_pme and g_pme_error, which give you performance and
> accuracy of
> the parameters, respectively.
> 
> So perhaps with some more information I can provide more help.
> 
> /Flo
> 
> >
> > Thanks!
> > Denzil Frost 
> > --
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> the
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Re: [gmx-users] rerun problem

[Mark Abraham]

On 25/02/2012 9:07 PM, ahmet yıldırım wrote:

Dear users,

I am using Gromacs 4.5.4. I rerun the simulation using the following 
command:

mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append
Unfortunately remaining output didnt append to existing files 
(protein-RUN.xtc, protein-RUN.edr,
protein-RUN.log). On the contrary remaining output appended to new 
files (traj.xtc, ener.edr, md.log).


You told mdrun on the command line to use the default filenames, so it 
did. Either specify the files you want appended, or use -deffnm 
suitably. Note that -deffnm cannot supply a name for -cpi.


Mark
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Re: [gmx-users] Re: gmx-users Digest, Vol 94, Issue 159

[Mark Abraham]

On 25/02/2012 6:45 PM, priya thiyagarajan wrote:

hello sir,

Thanks for your kind reply..

one small doubt sir.. its enough to give*mdrun -s md.tpr -cpi state.cpt
*
so that it ll automatically append my new data to the respective file  ..


Only if you are happy with the default filenames.

Mark
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Re: [gmx-users] gromacs: pdb2gmx error

[Mark Abraham]

On 25/02/2012 6:30 PM, venkatesh s wrote:

Hi
  i got that error in the step of pdb2gmx what can i do
i read also 
http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database

can any one tell exact reason and how i handle further


The exact reason is on that link. You will need to read it and think 
about what it means. If it doesn't mean anything, then you need to learn 
some more in chapter 5 of the manual (and/or the links in that web page 
section) about how things work.


Mark
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Re: [gmx-users] rc or rlist in minimum image convention?

[Justin A. Lemkul]

Juliette N. wrote:



On 24 February 2012 16:52, Justin A. Lemkul > wrote:




Juliette N. wrote:



On 23 February 2012 21:18, Mark Abraham mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 24/02/12, *"Juliette N." *mailto:joojoojo...@gmail.com>
   >__> wrote:



   On 23 February 2012 20:07, Mark Abraham
mailto:mark.abra...@anu.edu.au>
   >> wrote:

   On 24/02/2012 10:55 AM, Juliette N. wrote:

   Hi all,

   My average size is 2.9 nm obtained from NPT under
large
   pressure and now I intend  to increase rc to 1.4
and rlist to
   1.65 nm. I am just worried about violating
minimum image
   convention.


   That probably violates the parametrization of your
force field.

   Thanks Mark. You mean rc =1.4 for OPLS-AA is not
appropriate? In
   the original OPLSAA:   Optimized Intermolecular Potential
   Functions for Liquid Hydrocarbons
   I see rc of 15 A has been used for alkanes which requires
rlist of
   around 15+2.5+17.5 A ! Please comment why I am violating
   parametrization? Thanks.

It is appropriate to use a set of .mdp parameters that
most closely
   reproduce the parametrization conditions, or other conditions
that
   have been shown to be effective. So if you were using rc<1.4
and now
   want to use rc=1.4, then it is likely that at least one of those
   choices is inappropriate. If 1.5nm was used in parameterization,
   then both the foregoing are probably unsuitable. The values for
   other rxxx parameters should be addressed in that work, and will
   depend on charge group size and electrostatics model.


Thank you Mark. I was using rc =1.1 and just wanted to how much
my results vary by applying rc of 1.4 nm. I dont know the exact
value that was used in parametrization. I have just seen some
previous works with cut offs around these values. Is there
anyway I can obtain plot of LJ potential versus distance?



For any sigma and epsilon values, you can obtain such a plot with
g_sigeps.

The problem with the original OPLS parameterization was that
different cutoffs were used for different types of molecules.
 Shifted potentials were used instead of PME, which can change the
way electrostatics are handled if using the latter method.  Probably
someone, somewhere along the way, has published recommendations for
normal use in whatever type of system you're dealing with.


Thank you Justin.

1- The input values to g_sigeps has to be the geometric mean of two 
materials then?




I think g_sigeps is designed to produce simple plots for single atom types, but 
I suppose you can tweak it.  If you're looking for a simple difference in energy 
based on distance, you can do that in a few moments with a calculator and the 
Lennard-Jones equation.


I have also another trivial question. The OPLS 1984 paper, Optimized 
Intermolecular Potential Functions for Liquid

Hydrocarbons states:

The cutoff distance for the intermolecular interactions was a little 
less than half the average length of an edge of the periodic
cube. It ranged from 9.5 A, for methane to 13 A, for benzene and 15 A, 
for n-hexane.


My enquiry is that,

2-is this cutoff mentioned above the parametrization cutoff or the 
cutoff that has only been used in that paper?




Hence the problem with using OPLS, in some cases.  That paper was probably for 
the old OPLS-UA parameters (which are part of Gromacs, but are outdated) and 
exemplifies how each system differed in terms of cutoffs.


3- If thats the cutoff that was used in parametrization, since atom 
types of hexane, propane, heptane, and even saturated polymers 
C-C-C-CC are identical in atp file, does this mean for all 
alkanes and such polymers  rc =15 A must be used?
 


Again it depends on the nuts and bolts of the simulation.  The paper you cite is 
quite old and thus more modern algorithms for electrostatics, energy 
conservation, etc were not available.  I'd do some digging into more recent 
literature from people who have done similar things to see what they recommend. 
 For proteins, rc=rvdw=rlist=1.0 works well in conjunction with PME for 
electrostatics.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemi

[gmx-users] about periodicity removal

[rama david]

Hi GROMACS friends,
 I am trying to put to peptide close to each other..
with the help of -editconf  -ci and  -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
 To solve problem I proceed as  follow...
1. I make gro file , with the -editconf I make box and put molecule in
center
I get the box vectors and center co-ordinates.
2. then again with the help of editconf I make a another box of same vectors
   but slightly different center co-ordinates.(Distance is as per my
requirement)
3 Now have two gro files of box molecule ,having same box vectors and
different
   center.
4 I converted both  gro files to pdb files ,and catenate them to make
single pdb file.
5  Now I get the two molecule close enough to form hydrogen bond..
   but the problem is to convert it again into gro file and
generate topology
file , should I removed periodicity of molecule (As it showing the periodic
box in pymol)???
If it is , how to remove periodicity???
 Thank you for help
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Re: [gmx-users] about periodicity removal

[Justin A. Lemkul]

rama david wrote:

Hi GROMACS friends,
 I am trying to put to peptide close to each other..
with the help of -editconf  -ci and  -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
 To solve problem I proceed as  follow...
1. I make gro file , with the -editconf I make box and put molecule in 
center

I get the box vectors and center co-ordinates.
2. then again with the help of editconf I make a another box of same vectors
   but slightly different center co-ordinates.(Distance is as per my 
requirement)
3 Now have two gro files of box molecule ,having same box vectors and 
different

   center.
4 I converted both  gro files to pdb files ,and catenate them to make 
single pdb file.

5  Now I get the two molecule close enough to form hydrogen bond..
   but the problem is to convert it again into gro file and 
generate topology


It is easier to not generate a topology from this file.  If the peptides are 
identical, run a coordinate file of *one* of them through pdb2gmx and obtain its 
topology.  Then simply update the number of protein molecules in the [molecules] 
directive to reflect that the new system has two.


file , should I removed periodicity of molecule (As it showing the 
periodic box in pymol)???

If it is , how to remove periodicity???


What periodicity do you want to remove?  You have two peptides in a box, there's 
nothing to do there.


-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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[gmx-users] about periodicity removal....

[rama david]

Hi GROMACS friend,
  Thank you Justin For guidance.
 As I also doing your KALP-15 in DPPC tutorial,
In that you maintain remove initial periodicity of
DPPC..
  What is means initial periodicity??
That is the reason I thought the peptides have
Initial periodicity.(As periodic box is seen in pymol)..!!!

Thank you in advance
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Re: [gmx-users] about periodicity removal....

[Justin A. Lemkul]

rama david wrote:

Hi GROMACS friend,
  Thank you Justin For guidance.
 As I also doing your KALP-15 in DPPC tutorial,
In that you maintain remove initial periodicity of
DPPC.. 
  What is means initial periodicity??


The molecules of DPPC were post-processed in such a way that their atoms were 
split across periodic boundaries.



That is the reason I thought the peptides have
Initial periodicity.(As periodic box is seen in pymol)..!!!



The fact that you can see (or render) a periodic box is not a problem, quite the 
contrary.  Using periodic boundary conditions is commonplace, but only in 
certain situations is it necessary to undo their effects.  It does not sound to 
me like this is the case in your situation.


-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] Re: Internal water in the membrane receptor

[James Starlight]

Today I've tried to model internal water and forced with some problems :)

I've built my system by transferring water from X-ray structure to my
model. Than I've minimized this new structure in vacuum and water still
present on the desired positions

1) But when I've made my complete system ( with membrane mimicking Ccl4
layer) I've obtained this strange error during MDrun of this whole system (
there are no any errors during gromp pre-processing)

Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.


My topology has the below constracton

[ molecules ]
; Compound#mols
Protein 1
XW  16
Ccl4804
SOL 9884

where XW is the new .itp made for internal water based on SPC.itp

I dont know what exactly this strange error means and how to fix it :(


2) Also when I've changed protonation state of two ASP residues all
internal water left protein interior diffusing in the interiour during in
vacuum minimisation :)
I've tried to apply POSRES of that internal water but another eror occur

[ file posre_XW.itp, line 5 ]:
Atom index (4229) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section
"position_restraints"

I've checked posre_XW.itp file and didnt find any errors! The atom numbers
in posres are correspond to the atom nymbers in the GRO file. Why this
error might occur?

my topology
; Include X-ray water topology
#include "XW.itp"

; Include Position restraint for XW
#ifdef POSRES_XW
#include "posre_XW.itp"
#endif

my mdp
define= -DPOSRES_XW
integrator= steep

James

2012/2/25 Mark Abraham 

> On 25/02/2012 5:37 AM, James Starlight wrote:
>
>> Mark,
>>
>>
>> So as I understood the ussage of X-ray structure as the starting model
>> where the internal water is already present might be good in case to avoid
>> those sterric issues doesn't it ?
>>
>
> Yes. This was one of the options I suggested earlier.
>
>
>
>> What are additional options should I use for preparation of such system
>> with pdb2gmx ? Should I use posres on the internal water  ( e.g on oxygen
>> atoms) during energy minimisation and equilibration phases?
>>
>
> You probably do want a contiguous block of atoms with position restraints.
> That will require you have two different [moleculetype] sections for the
> different "kinds" of water, since the [position_restraints] section applies
> to all instances of its [moleculetype], and you will need to disable
> [settle] for at least one of those. It might be easier not to use separate
> restraints for a subset of water.
>
> Mark
>
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Re: [gmx-users] Re: Internal water in the membrane receptor

[Justin A. Lemkul]

James Starlight wrote:

Today I've tried to model internal water and forced with some problems :)

I've built my system by transferring water from X-ray structure to my 
model. Than I've minimized this new structure in vacuum and water still 
present on the desired positions


1) But when I've made my complete system ( with membrane mimicking Ccl4 
layer) I've obtained this strange error during MDrun of this whole 
system ( there are no any errors during gromp pre-processing)


Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.


My topology has the below constracton

[ molecules ]
; Compound#mols
Protein 1
XW  16
Ccl4804
SOL 9884

where XW is the new .itp made for internal water based on SPC.itp

I dont know what exactly this strange error means and how to fix it :(




You likely have a [settles] directive applied the the XW molecules (crystal 
waters, yes?) and SOL.  You can't do that.  The block of molecules to which 
[settles] are applied must be continuous.  You'll have to replace the [settles] 
directive in XW with normal constraints.  Mark already told you this in the last 
message.


2) Also when I've changed protonation state of two ASP residues all 
internal water left protein interior diffusing in the interiour during 
in vacuum minimisation :)

I've tried to apply POSRES of that internal water but another eror occur

[ file posre_XW.itp, line 5 ]:
Atom index (4229) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section 
"position_restraints"


I've checked posre_XW.itp file and didnt find any errors! The atom 
numbers in posres are correspond to the atom nymbers in the GRO file. 
Why this error might occur?




Your numbering is wrong.  Numbering within a [position_restraints] directive has 
nothing to do with the .gro file, and is based on the numbering of the atoms in 
a [moleculetype].


-Justin


my topology
; Include X-ray water topology
#include "XW.itp"

; Include Position restraint for XW
#ifdef POSRES_XW
#include "posre_XW.itp"
#endif

my mdp
define= -DPOSRES_XW
integrator= steep

James

2012/2/25 Mark Abraham >


On 25/02/2012 5:37 AM, James Starlight wrote:

Mark,


So as I understood the ussage of X-ray structure as the starting
model where the internal water is already present might be good
in case to avoid those sterric issues doesn't it ?


Yes. This was one of the options I suggested earlier.



What are additional options should I use for preparation of such
system with pdb2gmx ? Should I use posres on the internal water
 ( e.g on oxygen atoms) during energy minimisation and
equilibration phases?


You probably do want a contiguous block of atoms with position
restraints. That will require you have two different [moleculetype]
sections for the different "kinds" of water, since the
[position_restraints] section applies to all instances of its
[moleculetype], and you will need to disable [settle] for at least
one of those. It might be easier not to use separate restraints for
a subset of water.

Mark

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Department of Biochemistry
Virginia Tech
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[gmx-users] gromacs installation with mpi

[Sanku M]

Hi,
 I am using a cluster where user/local/bin has some old mpi executable. But, I 
have installed openmpi-1.3 in my own home directory so that I can use that for 
installing gromacs4.5.4 parallel version. I have also updated the path with the 
openmpi bin directory and library directory in the bash profile.

But, each time, I try to configure gromacs4.5.4 using enable-mpi mode, it 
always looks into the mpi installed in /usr/local/bin directory anad crashes 
saying that the mpicc is not compatible.
I wonder whether there is any particular flag I can use so that I can force 
gromacs to look for openmpi bin and lib folder installed in my home directory.
Thanks
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Re: [gmx-users] gromacs installation with mpi

[Justin A. Lemkul]

Sanku M wrote:

Hi,
 I am using a cluster where user/local/bin has some old mpi executable. 
But, I have installed openmpi-1.3 in my own home directory so that I can 
use that for installing gromacs4.5.4 parallel version. I have also 
updated the path with the openmpi bin directory and library directory in 
the bash profile.


But, each time, I try to configure gromacs4.5.4 using enable-mpi mode, 
it always looks into the mpi installed in /usr/local/bin directory anad 
crashes saying that the mpicc is not compatible.
I wonder whether there is any particular flag I can use so that I can 
force gromacs to look for openmpi bin and lib folder installed in my 
home directory.


Are you using cmake or autoconf?  Providing your actual commands here would be 
useful.  The approach is different based on your method of configuration, but 
with cmake you can set -DMPI_COMPILER=/path/to/mpicc or with similarly with 
autoconf, use the MPICC environment variable to point to the mpicc of choice.


-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] gromacs installation with mpi

[Justin A. Lemkul]

Sanku M wrote:

Hi,
  I intially tried the following command line for config log:
./configure --prefix=/home/berne/jm3745/UTIL/GROMACS_4.5.4_MPI/ 
--program-suffix=_4mpi --disable-shared -enable-mpi


and in the bash_profile I had set the path for my desired mpi executable:
PATH=$PATH:/home/berne/jm3745/UTIL/OPENMPI/bin:$HOME/bin:/home/berne/jm3745/UTIL/fftw/bin:
export CPPFLAGS=-I/home/berne/jm3745/UTIL/fftw/include
export 
LDFLAGS=-L/home/berne/jm3745/UTIL/fftw/lib:/home/berne/jm3745/UTIL/OPENMPI/lib


But, the program crashes saying that 'can not compile or link using mpicc'.
Looking inside config.log file, I found the following details:
configure:5396: checking for mpicc
configure:5412: found /usr/local/bin/mpicc
configure:5423: result: mpicc
configure:5438: checking whether the MPI cc command works
configure:5452: mpicc -o conftest -g -O2 
-I/home/berne/jm3745/UTIL/fftw/include 
-L/home/berne/jm3745/UTIL/fftw/lib:/home/berne/jm3745/UTIL/OPENMPI/lib 
conftest.c  >&5
/usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
searching for -lmpich
/usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
searching for -lmpich

/usr/bin/ld: cannot find -lmpich
collect2: ld returned 1 exit status
configure:5452: $? = 1

So, apparently, the program is searching for mpicc in /usr/local/bin 
directory for mpicc in stead of ~/UTIL/openmpi/bin directory which I 
hoped for.


So, then I tried another options for configuring using following command 
( by putting CC to be  ~/UTIL/openmpi/bin/mpicc)
./configure --prefix=/home/berne/jm3745/UTIL/GROMACS_4.5.4_MPI/ 
--program-suffix=_4mpi --disable-shared -enable-mpi 
CC= ~/UTIL/openmpi/bin/mpicc


But, here again, I got the same error: ''can not compile or link using 
mpicc'.
Now, looking inside the config.log, I find the exactly same problem as 
earlier: it still recognizes mpicc from /usr/local/bin:

and config.log says:
configure:5396: checking for mpicc
configure:5412: found /usr/local/bin/mpicc
configure:5423: result: mpicc
configure:5438: checking whether the MPI cc command works
configure:5452: mpicc -o conftest -g -O2 
-I/home/berne/jm3745/UTIL/fftw/include 
-L/home/berne/jm3745/UTIL/fftw/lib:/home/berne/jm3745/UTIL/OPENMPI/lib 
conftest.c  >&5
/usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
searching for -lmpich
/usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
searching for -lmpich

/usr/bin/ld: cannot find -lmpich
collect2: ld returned 1 exit status

So, no matter what I do, it just does not recognize anything else other 
than /usr/local/bin.

Any help will be highly appreciated.


You're using the wrong environment variable.  Use MPICC, not CC.

-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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[gmx-users] gromacs: pdb2gmx error

[venkatesh s]

Thanking you Mark Abraham for your valuable suggestion
Here i used DNA Ligand Complex only is that any specific options is there?

Thanks



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II M.Sc Bioinformatics,
Alagappa University,
Karaikudi-630003
Tamil Nadu,
India
svenkateshbioinformat...@gmail.com
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[gmx-users] Wall potential

[Abhijeet Joshi]

Hi Gomacians,

I want to use implicit wall.

I set the mdp parameters as follows.

nwall= 2
wall_type= 9-3
wall_r_linpot= 1
wall_atomtype= Au Au
wall_density = 58.01 58.01
wall_ewald_zfac  = 3

Also set LJ parameters in topology file.
Au196.9665 0.000  A 6.53000e-02 3.40800e-01  ; Gold

However,

In mdout file i get

   nwall= 2
   wall_type= 9-3
   wall_atomtype[0] = 7#why 7?
   wall_atomtype[1] = 7
   wall_density[0]  = 58.01
   wall_density[1]  = 58.01
   wall_ewald_zfac  = 3
   System-wall00.0e+00   -1.17533e+020.0e+000.0e+00
   System-wall10.0e+00   -2.41204e-010.0e+000.0e+00
wall0-wall00.0e+000.0e+000.0e+000.0e+00
wall0-wall10.0e+000.0e+000.0e+000.0e+00
wall1-wall10.0e+000.0e+000.0e+000.0e+00

Is this an error? can somebody tell me how 9-3 wall parameters are
calculated in gromacs?
Do I need to specify anything else?

Thanks in advance
-- 
 Abhijeet
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Re: [gmx-users] gromacs: pdb2gmx error

[Mark Abraham]

On 26/02/2012 3:13 PM, venkatesh s wrote:

Thanking you Mark Abraham for your valuable suggestion
Here i used DNA Ligand Complex only is that any specific options is there?


Please consider the advice here http://www.gromacs.org/Support about the 
kind of content that requests for help should have in order to maximize 
the chance that someone might be able to help you.


Mark
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[gmx-users] error

[dina dusti]

Dear Gromacs Specialists,

My total time for simulation is 60 ps (600 ns) because I work with MARTINI 
coarse-grained force field and this time is enough for my system, but when I do 
g_analyze -ee, I take this warning:  


Warning: tau2 is longer than the length of the data (864000)
the statistics might be bad

Should I increase the total time of simulation but this time is enough?!
Please help me.
Thanks in advance.
Best Regards
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Re: [gmx-users] error

[Mark Abraham]

On 26/02/2012 3:58 PM, dina dusti wrote:

Dear Gromacs Specialists,

My total time for simulation is 60 ps (600 ns) because I work with 
MARTINI coarse-grained force field and this time is enough for my system,


Different observables converge over different time scales. The 
autocorrelation time of potential energy in a fine-grained force field 
is around 1ps, but that of the kinetic energy is very much shorter. 
Atomic positions normally much longer.



but when I do g_analyze -ee, I take this warning:

Warning: tau2 is longer than the length of the data (864000)
the statistics might be bad

Should I increase the total time of simulation but this time is enough?!


We don't have any information with which to judge - and ultimately you 
will need to make this decision yourself.


Mark
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[gmx-users] error

[dina dusti]

Dear Mark,

Thank you very much from your response. 

Can you tell me what is the best solution for this warning, Please?

Warning: tau2 is longer than the length of the data (864000)
the statistics might be bad

In addition to this warning is related to error estimate for radius of gyration 
and momentum.

Thank you very much again.
Best Regards
Dina
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