date:20100709

[gmx-users] problem with angle restraints

2010-07-09 Thread subarna thakur

I trying to use angle restrain for an ligand molecule. I have included the 
following information in my .itp file of the ligand  -

[ angle_restraints ]
;  aiajak functc0c1c2c3
6 1 7 1  106.9510001
6 1 8 1  108.8310001
7 1 8 1  104.9610001
5 2 7 1  110.6610001
5 2 8 1  104.9810001
When I am running the grompp command , I am getting an error-
Incorrect number of parameters - found 2, expected 3 or 6 for Angle Rest..
--
I have gone through the manual it says that for angle restrains we have to 
provide the theta(degree);fc; multi.I have given all the relevant information 
but still there is error. Please tell me where I have gone wrong.

 Subarna Thakur

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Re: [gmx-users] the Pressure control in GROMACS 4.0.7

2010-07-09 Thread Justin A. Lemkul




zhongjin wrote:

Dear users,
I think the pressure control in gromacs 4.0.7 may have some 
problems. First ,The pressure value fluctuates widely ,even between 
-7984.377930 and 5920.053711 bar.Second,the average pressure sometimes 
is much larger than what I have set,for example, I have set ref_p  = 1.0 
, but the average is actually over 7 bar. It is because I have not set 
properly , or something else?


In the absence of your .mdp file and a more detailed description of your system, 
extent of equilibration, etc it's hard to make any judgment.  Wide fluctuations 
are not uncommon in relatively small systems:


http://www.gromacs.org/Documentation/Terminology/Pressure

-Justin


Zhongjin He


 



--


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] the Pressure control in GROMACS 4.0.7

2010-07-09 Thread zhongjin

Dear users,
    I think the pressure control in gromacs 4.0.7 may have some problems. 
First ,The pressure value fluctuates widely ,even between -7984.377930 and 
5920.053711 bar.Second,the average pressure sometimes is much larger than what 
I have set,for example, I have set ref_p  = 1.0 , but the average is actually 
over 7 bar. It is because I have not set properly , or something else?
Zhongjin He


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Re: [gmx-users] mdp file settings for PME

2010-07-09 Thread Justin A. Lemkul




jojo J wrote:

Dear experts,

I posted this message before but I think you did not see it since I 
noticed messages after this have been replied. I have a hydrocarbon 


Messages do not receive replies in any sort of order.  Probably no one has had 
any relevant comments yet, or they live in a time zone where they are not awake :)


system with no charged particles. Today In one of the GROMACS tutorials 
I saw the following setting in em.mdp file:

fourierspacing  =  0.12
;fourier_nx  =   0
;fourier_ny  =   0
;fourier_nz  =   0
;pme_order  =   4
;ewald_rtol =  1e-5
;optimize_fft  =  yes

has been used for PME . Sofar I did not even include coulombtype=PME in 
my em.mdp file. What I had was:

constraints =  all-bonds
integrator  =  steep
dt  =  0.002; ps !
nsteps  =  200
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1000.0

Can you please guide me whether it is necessary to include these lines 
in em file for system having only partial charges like hydrocarbon 
(alkane). Also, in md.mdp file I have only coulombtype=PME and not the 


This contradicts your statement above.  You said you had only uncharged 
particles, but clearly this is not the case.


above Ewald settings. Do you recommend to include those settings? 


For energy minimization, the effects of plain cutoffs may or may not be 
significant.  Using plain cutoffs for actual simulation is a bad idea.  The 
artifacts are well-documented and for modern simulations any good reviewer 
should raise an immediate concern if plain cutoffs were used and not thoroughly 
justified.  A method like PME is significantly more accurate, but you can also 
achieve reasonable results using switch, shift, etc.  Read about the relevant 
mechanics of the force field you're using for what might be appropriate.


Without the mentioned lines I am getting reasonabel results (potential 
energy, kinetic, ,, also T coupling works perfectly). If I had better to 
unclude them what is the best value for fourierspacing?




I don't think there's ever been any sort of systematic study on the effects of 
Fourier grid spacing.  The trade-off is between speed and accuracy.  Larger 
values speed up calculations, but make PME less accurate.  Smaller values have 
the opposite effect.  You could do a small test for yourself (0.12, 0.16, 
0.18...) to see if there are any adverse effects.


-Justin


Thank you,



--


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] pdb2gmx with DNA

2010-07-09 Thread Justin A. Lemkul




Patargias, George wrote:
Thanks for your reply Justin. 

I am trying to generate a topology dor a dna structure using the charmm dna.rtp 

I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for 
the 5' and 3' ends


I got this error 



Fatal error:
atom N not found in buiding block 2DG while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I quess I need to change something in the .rtp and/or the .tdb files. But what?



Maybe, maybe not.  It looks like pdb2gmx is trying to treat your DNA as protein. 
 What is your command line?  What are you choosing for termini?


-Justin


Thanks a lot

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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] Installing gromacs from git

2010-07-09 Thread Sai Pooja

Hi,

I had used the following steps to install a git version of gromacs.  It
installed correctly and I have been using it for a while. However, even
though I didnt install the parallel version, when I use mdrun it runs in
parallel. Is installation in the parallel mode by default? Is there a way to
use it without parallelization?

 301  cd gromacs
 302  ls
 303  export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"
 304  export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"
 305  clear
 306  ls
 307  ./configure --help
 308  ./configure --prefix=/fs/home/sm868/gromacsnew
 309  make &>log
 310  ls
 311  jmacs log
 312  grep "error" log
 313  grep "Error" log
 314  make install


Pooja

On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> For future reference, I was able to install gromacs and this is what
>> finally worked - installing gromacs in a folder different than the untared.
>> It somehow helped to not create the folder but just directly using the name
>> in the prefix
>>
>>  301  cd gromacs
>>  302  ls
>>  303  export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"
>>  304  export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"
>>  305  clear
>>  306  ls
>>  307  ./configure --help
>>  308  ./configure --prefix=/fs/home/sm868/gromacsnew
>>  309  make &>log
>>  310  ls
>>  311  jmacs log
>>  312  grep "error" log
>>  313  grep "Error" log
>>  314  make install
>>
>> I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew.
>> Make sure to update your PATH and MANPATH to find the
>> programs and unix manual pages, and possibly LD_LIBRARY_PATH
>> or /etc/ld.so.conf if you are using dynamic libraries.
>>
>>
>> Thanks for the help.
>> *One question - There is already another version of gromacs installed in
>> the /usr/local so I used a different directory to install it. Now do I need
>> to use "make links"?*
>>
>
> Do you normally make links?  If so, you'll be over-writing the executables
> in /usr/local/bin.  One other possible side effect is that if both
> /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't
> define which executable to use unambiguously without specifying the whole
> path name for each executable.
>
> If you're using several version of Gromacs concurrently on the same
> machine, it's probably best to just install them in their own locations and
> source the proper GMXRC when you log in to use the version you want.
>
> -Justin
>
>  *
>> *
>> Pooja
>>
>>
>>
>>
>>
>>
>> On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja > saipo...@gmail.com>> wrote:
>>
>>I redid the entire thing after that first mail in which i reported
>>the error related to fftw(including running the make uninstall
>>commands and removing the folders entirely and getting fresh ones).
>>I apologize for not specifying this and like I said... there seemed
>>to be no errors this time except when I ran make install for
>>gromacs. The error looks like this:
>> make[3]: *** [install-man1] Error 1
>> > make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
>> > make[2]: *** [install-am] Error 2
>> > make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
>> > make[1]: *** [install-recursive] Error 1
>> > make[1]: Leaving directory `/fs/home/sm868/gromacs/man'
>> > make: *** [install-recursive] Error 1
>>I didn't find any other error.. is there a way to look for them
>>other than looking at what is being printed while the command is
>>running? I tried $ grep "Error" */* in the folder but found nothing
>>more than entries in different scripts etc.
>>
>>
>>
>>
>>
>>
>>On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>> wrote:
>>
>>
>>
>>- Original Message -
>>From: Sai Pooja mailto:saipo...@gmail.com>>
>>Date: Sunday, June 20, 2010 15:09
>>Subject: Re: [gmx-users] Installing gromacs from git
>>To: Discussion list for GROMACS users >>
>>
>> > History log:
>>
>> > 189  ./configure --enable-threads --enable-float
>>--prefix=/fs/home/sm868/fftw-3.2.2
>> >   190  make
>> >   191  clear
>> >   192  make install
>> >   193  cd ..
>> >   194  cd gromacs
>> >   195  ls
>> >   196  export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"
>> >   197  export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"
>> >   198  ./bootstrap
>> >   199  ls
>> >   200  ./configure --prefix=/fs/home/sm868/gromacs
>> >   201  make
>> >   202  make install
>> >
>> > Everything works till I get the following error with make
>>install(after it runs for a while) :
>> > make[3]: *** [install-man1] Error 1
>> > make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'
>> > make[2]: *** [install-am] Error 2
>> > make[2]: Leaving directory `/fs/home

[gmx-users] pdb2gmx with DNA

2010-07-09 Thread Patargias, George

Thanks for your reply Justin. 

I am trying to generate a topology dor a dna structure using the charmm dna.rtp 

I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for 
the 5' and 3' ends

I got this error 


Fatal error:
atom N not found in buiding block 2DG while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I quess I need to change something in the .rtp and/or the .tdb files. But what?

Thanks a lot

George--
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[gmx-users] mdp file settings for PME

2010-07-09 Thread jojo J

Dear experts,

I posted this message before but I think you did not see it since I noticed
messages after this have been replied. I have a hydrocarbon system with no
charged particles. Today In one of the GROMACS tutorials I saw the following
setting in em.mdp file:
fourierspacing  =  0.12
;fourier_nx  =   0
;fourier_ny  =   0
;fourier_nz  =   0
;pme_order  =   4
;ewald_rtol =  1e-5
;optimize_fft  =  yes

has been used for PME . Sofar I did not even include coulombtype=PME in my
em.mdp file. What I had was:
constraints =  all-bonds
integrator  =  steep
dt  =  0.002; ps !
nsteps  =  200
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1000.0

Can you please guide me whether it is necessary to include these lines in em
file for system having only partial charges like hydrocarbon (alkane). Also,
in md.mdp file I have only coulombtype=PME and not the above Ewald settings.
Do you recommend to include those settings? Without the mentioned lines I am
getting reasonabel results (potential energy, kinetic, ,, also T coupling
works perfectly). If I had better to unclude them what is the best value for
fourierspacing?

Thank you,
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Re: [gmx-users] Missing sugar atom in CHARMM dna.rtp

2010-07-09 Thread Justin A. Lemkul




Patargias, George wrote:
Hi 

In the gromacs git version, I noticed that the sugar atom O2' is missing 
from the dna.rtp file...


No problem there, for deoxyribose.

-Justin



Best wishes 
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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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[gmx-users] Missing sugar atom in CHARMM dna.rtp

2010-07-09 Thread Patargias, George

Hi 

In the gromacs git version, I noticed that the sugar atom O2' is missing 
from the dna.rtp file...

Best wishes 
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[gmx-users] information regarding the bootstrap method implemented with the g_wham

2010-07-09 Thread Ozge Engin

Hi all,

I am trying to understand how the bootstrap method has been implemented
within the g_wham. Unfortunately, it is poorly documented in the help menu
and in the manual. I could not track of the options regarding the method.
Could anyone (maybe the one who has implemented the method) give a little
bit detailed information, please?

Thanks in advance

-- 
Ozge Engin
 ★☆
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Re: [gmx-users] fast rerun in order to get an energy

2010-07-09 Thread XAvier Periole

Reruns MUST use trr files. 

On Jul 9, 2010, at 19:04, "Jeffery Perkins"  wrote:

> I'm no expert but try a rerun, it will allow you to get at least the 
> potential energies for each frame in your trr or xtc file, I've never been 
> interested in kinetic for my reruns and as such am unsure how that would work 
> though it should be possible.  For this you'll need to build a slightly 
> different mdp file with at least the following options (other stuff should be 
> the same as in your initial run of this system)
> 
> nsteps = 0
> nxtenergy = 1
> 
> I usually turn the trr or xtc that I need to rerun into a gro file for input 
> using
> trjconv -f traj.trr -o out.gro -ndec 3
> 
> You then need to grompp this new mdp file something like:
> grompp -f rerun.mpd -p topol.top -c out.gro
> 
> and run an mdrun with the -rerun option turned on.
> 
> mdrun -rerun traj.trr
> 
> this should give you the energies at each frame in the normal ener.edr file 
> used by g_energy
> 
> May have missed something but this should be a good place to start looking, 
> best of luck,
> 
> Jeffery Perkins
> 
> -
> Magdalena  wrote:
> 
> Hi, i will be grateful for any clue.
> 
> Is it possible to extract an energy from finished trajectory? In my case the 
> trajectory wasn't leading with flag e so it's obvious that I haven't got any 
> edr files.
> I know that in log file there is some information about energy but I would 
> like to have it in one file. My trajectory is quite long so that why I 
> wouldn't like to start calcultations from the beginnig in order to achieve 
> right files. If somebody had a similar situation then would be so kind and 
> instruct me in right direction?
> Thanks in advance
> 
> --
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> 
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Re: [gmx-users] Solvating protein

2010-07-09 Thread Justin A. Lemkul

Sai Pooja wrote:

Now I use genion and it says no ions to add?

Using a coulomb cut-off of 1 nm
No ions to add and no potential to calculate.

command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o 
solions.gro -p finalnoss.top

You haven't told genion to add anything.  Use -np and/or -nn as appropriate.

-Justin

On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja > wrote:

I checked topology file but going with grompp makes sense. Thank you.

On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:

Sai Pooja wrote:

Well thats the thing. I have checked my pdb files. All
residues have

There aren't charges in a .pdb file, unless you've somehow added
them into one of the fields yourself.  The file you need to
check is your topology.  A running value of the net charges is
given in the [atoms] directive.  Charges are assigned by pdb2gmx
based on what is expected in the .rtp file and what you chose to
assign in terms of protonation state.

either 0 or integer net charges. The number 0.994 seems
like a rounding off error especially since the output of
genbox says that the system has zero net charge. Again, I
encounter this no-zero net charge

genbox reads coordinate files, so I don't know how any charge it
prints is meaningful.  It tells me there is a zero charge on a
lysozyme system that I know has a +8 charge (regardless of
whether or not I pass it a topology as well), so don't believe
genbox.  Believe grompp.  The magnitude is indeed due to small
rounding errors.  It should be interpreted as -1.

-Justin

when I run grompp with an mdp file for energy minimization
with the protein( excluding hydrogen ) restrained.

I am using the charmm implemented version of gromacs.

Pooja
On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 10/07/2010 1:28 AM, Sai Pooja wrote:

   Hi,

   When I start from a energy minimized protein in
vacuum and
   solvate it using genbox, the output message says that the
   protein has zero charge. So I skip the genion step. I
follow
   this with energy minimization of the solvated protein
followed
   by restraining the protein and then doing a short
mdrun (as is
   the usual procedure outlined in most tutorials).
However, when I
   run the grompp command as the first step for the position
   restrained md, it runs but prints a note saying that
the system
   has non-zero charge ~ -  0..

   NOTE 2 [file finalnoss.top, line 8070]:
System has non-zero total charge: -9.94e-01

   I dont understand. Do I need to run the genion step
anyway or is
   it okay to continue with this system?

   I'd believe grompp before genbox. Surely you know already
what is in
   your system, and thus its total charge. You should
already know the
   protonation state of all of your relevant protein
residues, because
   you made choices for them with pdb2gmx.

   Mark

   Pooja

   -- Quaerendo Invenietis-Seek and you shall
discover.

   -- Quaerendo Invenietis-Seek and you shall
discover.

   -- gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
http://www.gromacs.org/search before
   posting!
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   >.

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-- 
Quaerendo Invenietis-Seek and you shall discover.

-- 

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

Re: [gmx-users] Solvating protein

2010-07-09 Thread Sai Pooja

Now I use genion and it says no ions to add?

Using a coulomb cut-off of 1 nm
No ions to add and no potential to calculate.

command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o
solions.gro -p finalnoss.top


On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja  wrote:

> I checked topology file but going with grompp makes sense. Thank you.
>
>
> On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Sai Pooja wrote:
>>
>>> Well thats the thing. I have checked my pdb files. All residues have
>>>
>>
>> There aren't charges in a .pdb file, unless you've somehow added them into
>> one of the fields yourself.  The file you need to check is your topology.  A
>> running value of the net charges is given in the [atoms] directive.  Charges
>> are assigned by pdb2gmx based on what is expected in the .rtp file and what
>> you chose to assign in terms of protonation state.
>>
>>
>>  either 0 or integer net charges. The number 0.994 seems like a
>>> rounding off error especially since the output of genbox says that the
>>> system has zero net charge. Again, I encounter this no-zero net charge
>>>
>>
>> genbox reads coordinate files, so I don't know how any charge it prints is
>> meaningful.  It tells me there is a zero charge on a lysozyme system that I
>> know has a +8 charge (regardless of whether or not I pass it a topology as
>> well), so don't believe genbox.  Believe grompp.  The magnitude is indeed
>> due to small rounding errors.  It should be interpreted as -1.
>>
>> -Justin
>>
>>  when I run grompp with an mdp file for energy minimization with the
>>> protein( excluding hydrogen ) restrained.
>>>
>>> I am using the charmm implemented version of gromacs.
>>>
>>> Pooja
>>> On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham 
>>> >> mark.abra...@anu.edu.au>> wrote:
>>>
>>>On 10/07/2010 1:28 AM, Sai Pooja wrote:
>>>
>>>
>>>Hi,
>>>
>>>When I start from a energy minimized protein in vacuum and
>>>solvate it using genbox, the output message says that the
>>>protein has zero charge. So I skip the genion step. I follow
>>>this with energy minimization of the solvated protein followed
>>>by restraining the protein and then doing a short mdrun (as is
>>>the usual procedure outlined in most tutorials). However, when I
>>>run the grompp command as the first step for the position
>>>restrained md, it runs but prints a note saying that the system
>>>has non-zero charge ~ -  0..
>>>
>>>NOTE 2 [file finalnoss.top, line 8070]:
>>> System has non-zero total charge: -9.94e-01
>>>
>>>I dont understand. Do I need to run the genion step anyway or is
>>>it okay to continue with this system?
>>>
>>>
>>>I'd believe grompp before genbox. Surely you know already what is in
>>>your system, and thus its total charge. You should already know the
>>>protonation state of all of your relevant protein residues, because
>>>you made choices for them with pdb2gmx.
>>>
>>>Mark
>>>
>>>
>>>
>>>Pooja
>>>
>>>-- Quaerendo Invenietis-Seek and you shall discover.
>>>
>>>
>>>
>>>-- Quaerendo Invenietis-Seek and you shall discover.
>>>
>>>
>>>-- gmx-users mailing listgmx-users@gromacs.org
>>>
>>>
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search before
>>>posting!
>>>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
>>>
>>>
>>>
>>>
>>> --
>>> Quaerendo Invenietis-Seek and you shall discover.
>>>
>>>
>> --
>> 
>>
>> 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
>>
>> 
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> 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
>>
>
>
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
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Re: [gmx-users] Solvating protein

2010-07-09 Thread Sai Pooja

I checked topology file but going with grompp makes sense. Thank you.

On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> Well thats the thing. I have checked my pdb files. All residues have
>>
>
> There aren't charges in a .pdb file, unless you've somehow added them into
> one of the fields yourself.  The file you need to check is your topology.  A
> running value of the net charges is given in the [atoms] directive.  Charges
> are assigned by pdb2gmx based on what is expected in the .rtp file and what
> you chose to assign in terms of protonation state.
>
>
>  either 0 or integer net charges. The number 0.994 seems like a
>> rounding off error especially since the output of genbox says that the
>> system has zero net charge. Again, I encounter this no-zero net charge
>>
>
> genbox reads coordinate files, so I don't know how any charge it prints is
> meaningful.  It tells me there is a zero charge on a lysozyme system that I
> know has a +8 charge (regardless of whether or not I pass it a topology as
> well), so don't believe genbox.  Believe grompp.  The magnitude is indeed
> due to small rounding errors.  It should be interpreted as -1.
>
> -Justin
>
>  when I run grompp with an mdp file for energy minimization with the
>> protein( excluding hydrogen ) restrained.
>>
>> I am using the charmm implemented version of gromacs.
>>
>> Pooja
>> On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>On 10/07/2010 1:28 AM, Sai Pooja wrote:
>>
>>
>>Hi,
>>
>>When I start from a energy minimized protein in vacuum and
>>solvate it using genbox, the output message says that the
>>protein has zero charge. So I skip the genion step. I follow
>>this with energy minimization of the solvated protein followed
>>by restraining the protein and then doing a short mdrun (as is
>>the usual procedure outlined in most tutorials). However, when I
>>run the grompp command as the first step for the position
>>restrained md, it runs but prints a note saying that the system
>>has non-zero charge ~ -  0..
>>
>>NOTE 2 [file finalnoss.top, line 8070]:
>> System has non-zero total charge: -9.94e-01
>>
>>I dont understand. Do I need to run the genion step anyway or is
>>it okay to continue with this system?
>>
>>
>>I'd believe grompp before genbox. Surely you know already what is in
>>your system, and thus its total charge. You should already know the
>>protonation state of all of your relevant protein residues, because
>>you made choices for them with pdb2gmx.
>>
>>Mark
>>
>>
>>
>>Pooja
>>
>>-- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>>-- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>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
>>
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> 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
>
> 
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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Re: [gmx-users] fast rerun in order to get an energy

2010-07-09 Thread Jeffery Perkins

I'm no expert but try a rerun, it will allow you to get at least the potential 
energies for each frame in your trr or xtc file, I've never been interested in 
kinetic for my reruns and as such am unsure how that would work though it 
should be possible.  For this you'll need to build a slightly different mdp 
file with at least the following options (other stuff should be the same as in 
your initial run of this system)

nsteps = 0
nxtenergy = 1

I usually turn the trr or xtc that I need to rerun into a gro file for input 
using
trjconv -f traj.trr -o out.gro -ndec 3

You then need to grompp this new mdp file something like:
grompp -f rerun.mpd -p topol.top -c out.gro

and run an mdrun with the -rerun option turned on.

mdrun -rerun traj.trr

this should give you the energies at each frame in the normal ener.edr file 
used by g_energy

May have missed something but this should be a good place to start looking, 
best of luck,

Jeffery Perkins

-
Magdalena  wrote:

Hi, i will be grateful for any clue.

Is it possible to extract an energy from finished trajectory? In my case the 
trajectory wasn't leading with flag e so it's obvious that I haven't got any 
edr files.
I know that in log file there is some information about energy but I would like 
to have it in one file. My trajectory is quite long so that why I wouldn't like 
to start calcultations from the beginnig in order to achieve right files. If 
somebody had a similar situation then would be so kind and instruct me in right 
direction?
Thanks in advance

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Re: [gmx-users] Solvating protein

2010-07-09 Thread Justin A. Lemkul




Sai Pooja wrote:
Well thats the thing. I have checked my pdb files. All residues have 


There aren't charges in a .pdb file, unless you've somehow added them into one 
of the fields yourself.  The file you need to check is your topology.  A running 
value of the net charges is given in the [atoms] directive.  Charges are 
assigned by pdb2gmx based on what is expected in the .rtp file and what you 
chose to assign in terms of protonation state.


either 0 or integer net charges. The number 0.994 seems like a 
rounding off error especially since the output of genbox says that the 
system has zero net charge. Again, I encounter this no-zero net charge 


genbox reads coordinate files, so I don't know how any charge it prints is 
meaningful.  It tells me there is a zero charge on a lysozyme system that I know 
has a +8 charge (regardless of whether or not I pass it a topology as well), so 
don't believe genbox.  Believe grompp.  The magnitude is indeed due to small 
rounding errors.  It should be interpreted as -1.


-Justin

when I run grompp with an mdp file for energy minimization with the 
protein( excluding hydrogen ) restrained.


I am using the charmm implemented version of gromacs.

Pooja 

On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham > wrote:


On 10/07/2010 1:28 AM, Sai Pooja wrote:


Hi,

When I start from a energy minimized protein in vacuum and
solvate it using genbox, the output message says that the
protein has zero charge. So I skip the genion step. I follow
this with energy minimization of the solvated protein followed
by restraining the protein and then doing a short mdrun (as is
the usual procedure outlined in most tutorials). However, when I
run the grompp command as the first step for the position
restrained md, it runs but prints a note saying that the system
has non-zero charge ~ -  0..

NOTE 2 [file finalnoss.top, line 8070]:
 System has non-zero total charge: -9.94e-01

I dont understand. Do I need to run the genion step anyway or is
it okay to continue with this system?


I'd believe grompp before genbox. Surely you know already what is in
your system, and thus its total charge. You should already know the
protonation state of all of your relevant protein residues, because
you made choices for them with pdb2gmx.

Mark



Pooja

-- 
Quaerendo Invenietis-Seek and you shall discover.




-- 
Quaerendo Invenietis-Seek and you shall discover.



-- 
gmx-users mailing listgmx-users@gromacs.org


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Please search the archive at http://www.gromacs.org/search before
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.
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--
Quaerendo Invenietis-Seek and you shall discover.



--


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] Solvating protein

2010-07-09 Thread Sai Pooja

Well thats the thing. I have checked my pdb files. All residues have either
0 or integer net charges. The number 0.994 seems like a rounding off
error especially since the output of genbox says that the system has zero
net charge. Again, I encounter this no-zero net charge when I run grompp
with an mdp file for energy minimization with the protein( excluding
hydrogen ) restrained.

I am using the charmm implemented version of gromacs.

Pooja

On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham wrote:

> On 10/07/2010 1:28 AM, Sai Pooja wrote:
>
>>
>> Hi,
>>
>> When I start from a energy minimized protein in vacuum and solvate it
>> using genbox, the output message says that the protein has zero charge. So I
>> skip the genion step. I follow this with energy minimization of the solvated
>> protein followed by restraining the protein and then doing a short mdrun (as
>> is the usual procedure outlined in most tutorials). However, when I run the
>> grompp command as the first step for the position restrained md, it runs but
>> prints a note saying that the system has non-zero charge ~ -  0..
>>
>> NOTE 2 [file finalnoss.top, line 8070]:
>>  System has non-zero total charge: -9.94e-01
>>
>> I dont understand. Do I need to run the genion step anyway or is it okay
>> to continue with this system?
>>
>
> I'd believe grompp before genbox. Surely you know already what is in your
> system, and thus its total charge. You should already know the protonation
> state of all of your relevant protein residues, because you made choices for
> them with pdb2gmx.
>
> Mark
>
>
>
>> Pooja
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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
>



-- 
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-- 
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Re: [gmx-users] fast rerun in order to get an energy

2010-07-09 Thread Justin A. Lemkul




Magdalena wrote:

Hi, i will be grateful for any clue.

Is it possible to extract an energy from finished trajectory? In my case the
trajectory wasn't leading with flag e so it's obvious that I haven't got any
edr files. I know that in log file there is some information about energy but


You didn't get an .edr file at all?  Did you specify nstenergy > 0 in the .mdp 
file?  It seems odd that you didn't get anything.  The .edr file is a standard 
output file, there is no need to specify any flag to cause it to be written.



I would like to have it in one file. My trajectory is quite long so that why
I wouldn't like to start calcultations from the beginnig in order to achieve
right files. If somebody had a similar situation then would be so kind and
instruct me in right direction? Thanks in advance



You can pass your trajectory file to mdrun -rerun and it will recalculate the 
energies.


-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] fast rerun in order to get an energy

2010-07-09 Thread Magdalena

Hi, i will be grateful for any clue.

Is it possible to extract an energy from finished trajectory? In my case the 
trajectory wasn't leading with flag e so it's obvious that I haven't got any 
edr files.
I know that in log file there is some information about energy but I would like 
to have it in one file. My trajectory is quite long so that why I wouldn't like 
to start calcultations from the beginnig in order to achieve right files. If 
somebody had a similar situation then would be so kind and instruct me in right 
direction?
Thanks in advance

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Frozen N2 in a very long tube

2010-07-09 Thread shuai shuai

Hear all,

Recently I met a strong error from gromacs. Therefore I would like to know
whether you have experienced the same thing or what is the reason for that.

The system I simulated is nvt MD for N2 (with partial charge) diffusion in a
long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a
small cluster after a few ns. The weird thing is that I do not have
such problem for either longer domain or short domain.  The input
parameters are:

title= CNT
; Preprocessor - specify a full path if necessary.
cpp  = /lib/cpp
include  =
define   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 1000
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 10
nstvout  = 10
nstfout  = 10
; Checkpointing helps you continue after crashes
nstcheckpoint= 10
; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 1
xtc-precision= 100

; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 1.0
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = nose-hoover
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 1
ref_t= 303.15
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 5
compressibility  = 4.5e-5
ref_p= 1
; Random seed for Andersen thermostat
andersen_seed= 815131
; OPTIONS FOR BONDS
constraints  = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start  = no
; Use successive overrelaxation to reduce the number of shake iterat

Re: [gmx-users] Solvating protein

2010-07-09 Thread Mark Abraham


On 10/07/2010 1:28 AM, Sai Pooja wrote:


Hi,

When I start from a energy minimized protein in vacuum and solvate it 
using genbox, the output message says that the protein has zero 
charge. So I skip the genion step. I follow this with energy 
minimization of the solvated protein followed by restraining the 
protein and then doing a short mdrun (as is the usual procedure 
outlined in most tutorials). However, when I run the grompp command as 
the first step for the position restrained md, it runs but prints a 
note saying that the system has non-zero charge ~ -  0..


NOTE 2 [file finalnoss.top, line 8070]:
  System has non-zero total charge: -9.94e-01

I dont understand. Do I need to run the genion step anyway or is it 
okay to continue with this system?


I'd believe grompp before genbox. Surely you know already what is in 
your system, and thus its total charge. You should already know the 
protonation state of all of your relevant protein residues, because you 
made choices for them with pdb2gmx.


Mark



Pooja

--
Quaerendo Invenietis-Seek and you shall discover.



--
Quaerendo Invenietis-Seek and you shall discover.


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[gmx-users] Solvating protein

2010-07-09 Thread Sai Pooja

Hi,

When I start from a energy minimized protein in vacuum and solvate it using
genbox, the output message says that the protein has zero charge. So I skip
the genion step. I follow this with energy minimization of the solvated
protein followed by restraining the protein and then doing a short mdrun (as
is the usual procedure outlined in most tutorials). However, when I run the
grompp command as the first step for the position restrained md, it runs but
prints a note saying that the system has non-zero charge ~ -  0..

NOTE 2 [file finalnoss.top, line 8070]:
  System has non-zero total charge: -9.94e-01

I dont understand. Do I need to run the genion step anyway or is it okay to
continue with this system?

Pooja

-- 
Quaerendo Invenietis-Seek and you shall discover.



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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[gmx-users] Ewald setting for hydrocarbon system?

2010-07-09 Thread jojo J

Dear all,

I need your favor. I have a hydrocarbon system with no charged particles.
Today In one of the GROMACS tutorials I saw the following setting in em.mdp
file:
fourierspacing  =  0.12
;fourier_nx  =   0
;fourier_ny  =   0
;fourier_nz  =   0
;pme_order  =   4
;ewald_rtol =  1e-5
;optimize_fft  =  yes

has been used for PME . Sofar I did not even include coulombtype=PME in my
em.mdp file. What I had was:
constraints =  all-bonds
integrator  =  steep
dt  =  0.002; ps !
nsteps  =  200
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1000.0

Can you please guide me whether it is necessary to include these lines in em
file for system having only partial charges like hydrocarbon (alkane). Also,
in md.mdp file I have only coulombtype=PME and not the above Ewald settings.
Do you recommend to include those settings? Without the mentioned lines I am
getting reasonabel results (potential energy, kinetic, ,, also T coupling
works perfectly). If I had better to unclude them what is the best value for
fourierspacing?

Thank you,
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Re: [gmx-users] P4_error for extending coarse grained MD simulations

2010-07-09 Thread XAvier Periole



Do you have same problem if you use the state_prec.cpt?

Could it be just that file is corrupted for some reason ?

On Jul 9, 2010, at 11:29 AM, 张春雷 wrote:


Hi Carsten,

The error message I post is got on a single core with MPI.

p0_6991:  p4_error: interrupt SIGSEGV: 11

So it states p0_.

I dont think the error is due to the MPI progrom.
Am I right?

Justin Zhang

在 2010年7月9日 下午4:00，Carsten Kutzner 写道：
Hi Justin,

what kind of error message do you get if you run this system
on a single core without MPI?

Carsten


On Jul 8, 2010, at 9:36 PM, 张春雷 wrote:


Dear all,

I have post this question about a two weeks ago. During these days,  
I followed suggestions from Mark and weixin, but did not fix it.  
Here, I repeat it again to seek more help.


I attempt to extend MD simulation for a coarse-grained system. CG  
models are in MARTINI form. Simulation was carried out on Gromacs  
4.02, 4.03 or 4.07.


I tried to use check point file state.cpt to extend my simulation.  
The mdrun program can read to the check file. But it reported error  
like this:


Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010

Loaded with Money

starting mdrun 'Protein in POPE bilayer'
2400 steps, 72.0 ps (continuing from step 1200,  
36.0 ps).

step 1200, remaining runtime: 0 s
p0_6991:  p4_error: interrupt SIGSEGV: 11

I check the state.cpt file using gmxdump and compare it with other  
checkpoint files that can be used for extending All-atom  
simulations. I found that in the CG check point file, some sections  
are missing: box-v (3x3) and thermostat-integral.
I am not sure whether this missing sections cause my run crash. If  
it is, could any one tell me possible reasons that result in the  
loss of box-v and thermostat-integral and how to fix the problem?


Your suggestions are greatly helpful and appreciated.

Justin Zhang



在 2010年6月25日 下午4:45，张春雷 写道：
Information shown by gmxcheck:

Checking file state.cpt

# Atoms  9817
Last frame -1 time 36.000


Item#frames Timestep (ps)
Step 1
Time 1
Lambda   1
Coords   1
Velocities   1
Forces   0
Box  1

Checking file state_prev.cpt

# Atoms  9817
Last frame -1 time 359010.000


Item#frames Timestep (ps)
Step 1
Time 1
Lambda   1
Coords   1
Velocities   1
Forces   0
Box  1

Checking file md_360ns.trr
trn version: GMX_trn_file (double precision)
Reading frame   0 time0.000
# Atoms  9817
Reading frame2000 time 30.000


Item#frames Timestep (ps)
Step  2401150
Time  2401150
Lambda2401150
Coords2401150
Velocities2401150
Forces   0
Box   2401150

Is anything wrong?


2010/6/25 Mark Abraham 



- Original Message -
From: 张春雷 
Date: Friday, June 25, 2010 16:46
Subject: Re: [gmx-users] P4_error for extending coarse grained MD  
simulations

To: Discussion list for GROMACS users 

> The last .gro file only provides coordinates of the system. No  
velocity is recorded. Actually, what I attempt to achieve is a  
binary identical trajectory. So I think the velocity from the last  
step is critical.

>
> I have tried another approach in which the checkpoint file is  
neglected.

>
> $mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g  
md_720ns.log

>
> It works. So the checkpoint file appears to contain some error.  
But it is generated by a normally finished production simulation.


What does gmxcheck say about all the files involved?

Mark


> Have  you encountered similar things?
>
> Thank you for your suggestions!
>
>
>
> 在 2010年6月25日 上午9:16，weixin 写道：
>
> How about using the last .gro file to continue your simulation?
>
>
>
> 2010/6/24 张春雷 
> Dear GMX-users,
>
> This is Justin.
> I am performing coarse-grained simulation on a protein-lipid  
bilayer system. This is a MARTINI CG model.
> I have successfully completed a 360ns simulation, during which  
the time step is 30 fs.

>
> I would like to extend the simulation to 1micro-second. The  
commands I used are:

>
> $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
>
> $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o  
md_360ns.trr -g md_360ns.log -cpi state.cpt

>
> However, I received the following message:
>
> Checkpoint file is from part 1, new output files will be suffixed  
part0002.

> Getting Loaded...
> Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
>
> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10  
2010

>
> Loaded with Money
>
> starting mdrun 'Protein in POPE bilayer'
> 2400 steps, 72.0 ps (continuing from step 1200,  
36.0 ps).

> step 1200, remaining runtime: 0 s
> p0_6991:  p4_error: interrupt SIGSEGV: 11
>
> I have searched the mail-list, but found no similar report. I  
also search through google, but no answer seems satisf

Re: [gmx-users] P4_error for extending coarse grained MD simulations

2010-07-09 Thread Carsten Kutzner

On Jul 9, 2010, at 11:29 AM, 张春雷 wrote:

> Hi Carsten,
> 
> The error message I post is got on a single core with MPI.
> 
> p0_6991:  p4_error: interrupt SIGSEGV: 11
> 
> So it states p0_.
> 
> I dont think the error is due to the MPI progrom.
> Am I right?
Yes, but there must be some more diagnostic information from 
mdrun about what has gone wrong. Please check stderr / stdout
output files as well as md.log.

Carsten

 
> 
> Justin Zhang
> 
> 在 2010年7月9日 下午4:00，Carsten Kutzner 写道：
> Hi Justin,
> 
> what kind of error message do you get if you run this system
> on a single core without MPI?
> 
> Carsten
> 
> 
> On Jul 8, 2010, at 9:36 PM, 张春雷 wrote:
> 
>> Dear all,
>> 
>> I have post this question about a two weeks ago. During these days, I 
>> followed suggestions from Mark and weixin, but did not fix it. Here, I 
>> repeat it again to seek more help.
>> 
>> I attempt to extend MD simulation for a coarse-grained system. CG models are 
>> in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07.
>> 
>> I tried to use check point file state.cpt to extend my simulation. The mdrun 
>> program can read to the check file. But it reported error like this: 
>> 
>> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
>> 
>> Loaded with Money
>> 
>> starting mdrun 'Protein in POPE bilayer'
>> 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
>> step 1200, remaining runtime: 0 s  
>> p0_6991:  p4_error: interrupt SIGSEGV: 11
>> 
>> I check the state.cpt file using gmxdump and compare it with other 
>> checkpoint files that can be used for extending All-atom simulations. I 
>> found that in the CG check point file, some sections are missing: box-v 
>> (3x3) and thermostat-integral.
>> I am not sure whether this missing sections cause my run crash. If it is, 
>> could any one tell me possible reasons that result in the loss of box-v and 
>> thermostat-integral and how to fix the problem?
>> 
>> Your suggestions are greatly helpful and appreciated.
>> 
>> Justin Zhang
>>  
>> 
>> 
>> 在 2010年6月25日 下午4:45，张春雷 写道：
>> Information shown by gmxcheck:
>> 
>> Checking file state.cpt
>> 
>> # Atoms  9817
>> Last frame -1 time 36.000   
>> 
>> 
>> Item#frames Timestep (ps)
>> Step 1
>> Time 1
>> Lambda   1
>> Coords   1
>> Velocities   1
>> Forces   0
>> Box  1
>> 
>> Checking file state_prev.cpt
>> 
>> # Atoms  9817
>> Last frame -1 time 359010.000   
>> 
>> 
>> Item#frames Timestep (ps)
>> Step 1
>> Time 1
>> Lambda   1
>> Coords   1
>> Velocities   1
>> Forces   0
>> Box  1
>> 
>> Checking file md_360ns.trr
>> trn version: GMX_trn_file (double precision)
>> Reading frame   0 time0.000   
>> # Atoms  9817
>> Reading frame2000 time 30.000   
>> 
>> 
>> Item#frames Timestep (ps)
>> Step  2401150
>> Time  2401150
>> Lambda2401150
>> Coords2401150
>> Velocities2401150
>> Forces   0
>> Box   2401150
>> 
>> Is anything wrong? 
>> 
>> 
>> 2010/6/25 Mark Abraham 
>> 
>> 
>> 
>> - Original Message -
>> From: 张春雷 
>> Date: Friday, June 25, 2010 16:46
>> Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations
>> To: Discussion list for GROMACS users 
>> 
>> > The last .gro file only provides coordinates of the system. No velocity is 
>> > recorded. Actually, what I attempt to achieve is a binary identical 
>> > trajectory. So I think the velocity from the last step is critical.
>> > 
>> > I have tried another approach in which the checkpoint file is neglected.
>> > 
>> > $mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g 
>> > md_720ns.log
>> > 
>> > It works. So the checkpoint file appears to contain some error. But it is 
>> > generated by a normally finished production simulation.
>> 
>> What does gmxcheck say about all the files involved?
>> 
>> Mark
>> 
>> 
>> > Have  you encountered similar things?
>> > 
>> > Thank you for your suggestions!
>> >  
>> > 
>> > 
>> > 在 2010年6月25日 上午9:16，weixin 写道：
>> >  
>> > How about using the last .gro file to continue your simulation?
>> > 
>> > 
>> >  
>> > 2010/6/24 张春雷 
>> > Dear GMX-users,
>> > 
>> > This is Justin. 
>> > I am performing coarse-grained simulation on a protein-lipid bilayer 
>> > system. This is a MARTINI CG model.
>> > I have successfully completed a 360ns simulation, during which the time 
>> > step is 30 fs.
>> > 
>> > I would like to extend the simulation to 1micro-second. The commands I 
>> > used are:
>> > 
>> > $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
>> > 
>> > $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o md_360ns.trr -g 
>> > md_360ns.log -cpi state.cpt
>> > 
>> > However, I received the following message:
>> > 
>> > Checkpoint file is from part 1, new outp

Re: [gmx-users] P4_error for extending coarse grained MD simulations

2010-07-09 Thread 张春雷

Hi Carsten,

The error message I post is got on a single core with MPI.

p0_6991:  p4_error: interrupt SIGSEGV: 11

So it states p0_.

I dont think the error is due to the MPI progrom.
Am I right?

Justin Zhang

在 2010年7月9日 下午4:00，Carsten Kutzner 写道：

> Hi Justin,
>
> what kind of error message do you get if you run this system
> on a single core without MPI?
>
> Carsten
>
>
> On Jul 8, 2010, at 9:36 PM, 张春雷 wrote:
>
> Dear all,
>
> I have post this question about a two weeks ago. During these days, I
> followed suggestions from Mark and weixin, but did not fix it. Here, I
> repeat it again to seek more help.
>
> I attempt to extend MD simulation for a coarse-grained system. CG models
> are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or
> 4.07.
>
> I tried to use check point file state.cpt to extend my simulation. The
> mdrun program can read to the check file. But it reported error like this:
>
> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
>
> Loaded with Money
>
> starting mdrun 'Protein in POPE bilayer'
> 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
> step 1200, remaining runtime: 0 s
> p0_6991:  p4_error: interrupt SIGSEGV: 11
>
> I check the *state.cpt* file using *gmxdump* and compare it with other
> checkpoint files that can be used for extending All-atom simulations. I
> found that in the CG check point file, some sections are missing: *box-v
> (3x3)* and *thermostat-integral*.
> I am not sure whether this missing sections cause my run crash. If it is,
> could any one tell me possible reasons that result in the loss of box-v and
> thermostat-integral and how to fix the problem?
>
> Your suggestions are greatly helpful and appreciated.
>
> Justin Zhang
>
>
>
> 在 2010年6月25日 下午4:45，张春雷 写道：
>
>> Information shown by gmxcheck:
>>
>> *Checking file state.cpt*
>>
>> # Atoms  9817
>> Last frame -1 time 36.000
>>
>>
>> Item#frames Timestep (ps)
>> Step 1
>> Time 1
>> Lambda   1
>> Coords   1
>> Velocities   1
>> Forces   0
>> Box  1
>>
>> *Checking file state_prev.cpt*
>>
>> # Atoms  9817
>> Last frame -1 time 359010.000
>>
>>
>> Item#frames Timestep (ps)
>> Step 1
>> Time 1
>> Lambda   1
>> Coords   1
>> Velocities   1
>> Forces   0
>> Box  1
>>
>> *Checking file md_360ns.trr*
>> trn version: GMX_trn_file (double precision)
>> Reading frame   0 time0.000
>> # Atoms  9817
>> Reading frame2000 time 30.000
>>
>>
>> Item#frames Timestep (ps)
>> Step  2401150
>> Time  2401150
>> Lambda2401150
>> Coords2401150
>> Velocities2401150
>> Forces   0
>> Box   2401150
>>
>> Is anything wrong?
>>
>>
>> 2010/6/25 Mark Abraham 
>>
>>
>>>
>>> - Original Message -
>>> From: 张春雷 
>>> Date: Friday, June 25, 2010 16:46
>>> Subject: Re: [gmx-users] P4_error for extending coarse grained MD
>>> simulations
>>> To: Discussion list for GROMACS users 
>>>
>>> > The last .gro file only provides coordinates of the system. No
>>> velocity is recorded. Actually, what I attempt to achieve is a binary
>>> identical trajectory. So I think the velocity from the last step is
>>> critical.
>>> >
>>> > I have tried another approach in which the checkpoint file is
>>> neglected.
>>> >
>>> > $mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g
>>> md_720ns.log
>>> >
>>> > It works. So the checkpoint file appears to contain some error. But it
>>> is generated by a normally finished production simulation.
>>>
>>> What does gmxcheck say about all the files involved?
>>>
>>> Mark
>>>
>>>
>>> > Have  you encountered similar things?
>>> >
>>> > Thank you for your suggestions!
>>> >
>>> >
>>> >
>>> > 在 2010年6月25日 上午9:16，weixin 写道：
>>>
 >
 > How about using the last .gro file to continue your simulation?
 >
 >
 >
 > 2010/6/24 张春雷 

> > Dear GMX-users,
> >
> > This is Justin.
> > I am performing coarse-grained simulation on a protein-lipid bilayer
> system. This is a MARTINI CG model.
> > I have successfully completed a 360ns simulation, during which the
> time step is 30 fs.
> >
> > I would like to extend the simulation to 1micro-second. The commands
> I used are:
> >
> > $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
> >
> > $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o
> md_360ns.trr -g md_360ns.log -cpi state.cpt
> >
> > However, I received the following message:
> >
> > Checkpoint file is from part 1, new output files will be suffixed
> part0002.
> > Getting Loaded...
> > Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
> >
> > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10
> 2010
> >
> > Loaded

Re: [gmx-users] P4_error for extending coarse grained MD simulations

2010-07-09 Thread Carsten Kutzner

Hi Justin,

what kind of error message do you get if you run this system
on a single core without MPI?

Carsten


On Jul 8, 2010, at 9:36 PM, 张春雷 wrote:

> Dear all,
> 
> I have post this question about a two weeks ago. During these days, I 
> followed suggestions from Mark and weixin, but did not fix it. Here, I repeat 
> it again to seek more help.
> 
> I attempt to extend MD simulation for a coarse-grained system. CG models are 
> in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07.
> 
> I tried to use check point file state.cpt to extend my simulation. The mdrun 
> program can read to the check file. But it reported error like this: 
> 
> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
> 
> Loaded with Money
> 
> starting mdrun 'Protein in POPE bilayer'
> 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
> step 1200, remaining runtime: 0 s  
> p0_6991:  p4_error: interrupt SIGSEGV: 11
> 
> I check the state.cpt file using gmxdump and compare it with other checkpoint 
> files that can be used for extending All-atom simulations. I found that in 
> the CG check point file, some sections are missing: box-v (3x3) and 
> thermostat-integral.
> I am not sure whether this missing sections cause my run crash. If it is, 
> could any one tell me possible reasons that result in the loss of box-v and 
> thermostat-integral and how to fix the problem?
> 
> Your suggestions are greatly helpful and appreciated.
> 
> Justin Zhang
>  
> 
> 
> 在 2010年6月25日 下午4:45，张春雷 写道：
> Information shown by gmxcheck:
> 
> Checking file state.cpt
> 
> # Atoms  9817
> Last frame -1 time 36.000   
> 
> 
> Item#frames Timestep (ps)
> Step 1
> Time 1
> Lambda   1
> Coords   1
> Velocities   1
> Forces   0
> Box  1
> 
> Checking file state_prev.cpt
> 
> # Atoms  9817
> Last frame -1 time 359010.000   
> 
> 
> Item#frames Timestep (ps)
> Step 1
> Time 1
> Lambda   1
> Coords   1
> Velocities   1
> Forces   0
> Box  1
> 
> Checking file md_360ns.trr
> trn version: GMX_trn_file (double precision)
> Reading frame   0 time0.000   
> # Atoms  9817
> Reading frame2000 time 30.000   
> 
> 
> Item#frames Timestep (ps)
> Step  2401150
> Time  2401150
> Lambda2401150
> Coords2401150
> Velocities2401150
> Forces   0
> Box   2401150
> 
> Is anything wrong? 
> 
> 
> 2010/6/25 Mark Abraham 
> 
> 
> 
> - Original Message -
> From: 张春雷 
> Date: Friday, June 25, 2010 16:46
> Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations
> To: Discussion list for GROMACS users 
> 
> > The last .gro file only provides coordinates of the system. No velocity is 
> > recorded. Actually, what I attempt to achieve is a binary identical 
> > trajectory. So I think the velocity from the last step is critical.
> > 
> > I have tried another approach in which the checkpoint file is neglected.
> > 
> > $mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g 
> > md_720ns.log
> > 
> > It works. So the checkpoint file appears to contain some error. But it is 
> > generated by a normally finished production simulation.
> 
> What does gmxcheck say about all the files involved?
> 
> Mark
> 
> 
> > Have  you encountered similar things?
> > 
> > Thank you for your suggestions!
> >  
> > 
> > 
> > 在 2010年6月25日 上午9:16，weixin 写道：
> >  
> > How about using the last .gro file to continue your simulation?
> > 
> > 
> >  
> > 2010/6/24 张春雷 
> > Dear GMX-users,
> > 
> > This is Justin. 
> > I am performing coarse-grained simulation on a protein-lipid bilayer 
> > system. This is a MARTINI CG model.
> > I have successfully completed a 360ns simulation, during which the time 
> > step is 30 fs.
> > 
> > I would like to extend the simulation to 1micro-second. The commands I used 
> > are:
> > 
> > $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
> > 
> > $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o md_360ns.trr -g 
> > md_360ns.log -cpi state.cpt
> > 
> > However, I received the following message:
> > 
> > Checkpoint file is from part 1, new output files will be suffixed part0002.
> > Getting Loaded...
> > Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
> > 
> > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
> > 
> > Loaded with Money
> > 
> > starting mdrun 'Protein in POPE bilayer'
> > 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
> > step 1200, remaining runtime: 0 s  
> > p0_6991:  p4_error: interrupt SIGSEGV: 11
> > 
> > I have searched the mail-list, but found no similar report. I also search 
> > through google, but no answer seems satisfactory.
> > 
> > I once performed extending simulation for all atom si

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