Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Jianguo Li]

Dear all,

I have made a test calculation of local pressure using version 4.5 for my 
membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the 
localpressure data. Howeve, instead of giving an anveraged data of the local 
pressure, mdrun gives a separate file for each frame, so I got many files: 
localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 
..
Then I need to calculate the pressure tensor for each frame and make average. 
but  these localpressure.dat files are very big (each file is about 30 Mb), 
occupying large space of the hard disk. Can anyone give some suggestions on how 
to fix this? Thank you very much!

The command is: 
mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr  
-g md5_rerun.log -localpgrid 0.1
And the output message is:

Dumping local pressure based on 1 frames to localpressure.dat0...
Reading frame   2 time 119400.000   

Dumping local pressure based on 1 frames to localpressure.dat1...
Reading frame   3 time 119500.000   

Dumping local pressure based on 1 frames to localpressure.dat2...
Reading frame   4 time 119600.000   

Dumping local pressure based on 1 frames to localpressure.dat3...
Reading frame   5 time 119700.000   

Dumping local pressure based on 1 frames to localpressure.dat4...
Reading frame   6 time 119800.000   
...

Cheers,
Jianguo







From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Friday, 10 June 2011 07:10:35
Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5



Amit Choubey wrote:
> Thanks Justin, I tried to install the recent git version but the configure 
> file 
>is missing. How should I install this version ?
> 

Run the bootstrap script.  It generates the configure script.

-Justin

> 
> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul > wrote:
> 
> 
> 
> Amit Choubey wrote:
> 
> Dear all,
> 
> I saw an unanswered post at
>http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
> 
> It is about calculating local pressure in v 4.5 when using
> CHARMM FF. Could someone give me some pointers about this?
> 
> 
> I don't know what the development status of version 4.5 is, but you
> can access it at:
> 
>
>http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
> 
> It hasn't been merged with release-4-5-patches in some time, so many
> resolved bugs won't be fixed.
> 
> -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
> 
> 
> -- gmx-users mailing listgmx-users@gromacs.org
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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] local pressure calcuation for Gromacs-4.5

[Mark Abraham]

On 15/06/2011 9:09 PM, Jianguo Li wrote:

Dear all,

I have made a test calculation of local pressure using version 4.5 for 
my membrane simulation using CHARMM FF. When rerun the simulation, 
mdrun gives the localpressure data. Howeve, instead of giving an 
anveraged data of the local pressure, mdrun gives a separate file for 
each frame, so I got many files: localpressure.dat0, 
localpressure.dat1, localpressure.dat2, localpressure.dat3 ..
Then I need to calculate the pressure tensor for each frame and make 
average. but these localpressure.dat files are very big (each file is 
about 30 Mb), occupying large space of the hard disk. Can anyone give 
some suggestions on how to fix this? Thank you very much!


I would expect that the output frequency is configurable, but can only 
suggest you consult what documentation exists for this version. Your 
main alternatives are


* to compress the files with (say) bzip2 or (less effective) gzip and 
construct a script to uncompress them singly and analyse them "on the 
fly" (AMBER users do a bit of this kind of thing, Google around)
* to discard ones that are too frequent. However, judging from the 
numbers below, every 100ps is probably OK.


Mark


The command is:
mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o 
box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1

And the output message is:

Dumping local pressure based on 1 frames to localpressure.dat0...
Reading frame   2 time 119400.000

Dumping local pressure based on 1 frames to localpressure.dat1...
Reading frame   3 time 119500.000

Dumping local pressure based on 1 frames to localpressure.dat2...
Reading frame   4 time 119600.000

Dumping local pressure based on 1 frames to localpressure.dat3...
Reading frame   5 time 119700.000

Dumping local pressure based on 1 frames to localpressure.dat4...
Reading frame   6 time 119800.000
...

Cheers,
Jianguo




*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Friday, 10 June 2011 07:10:35
*Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5



Amit Choubey wrote:
> Thanks Justin, I tried to install the recent git version but the 
configure file is missing. How should I install this version ?

>

Run the bootstrap script.  It generates the configure script.

-Justin

>
> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul  >> wrote:

>
>
>
>Amit Choubey wrote:
>
>Dear all,
>
>I saw an unanswered post at
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
>
>It is about calculating local pressure in v 4.5 when using
>CHARMM FF. Could someone give me some pointers about this?
>
>
>I don't know what the development status of version 4.5 is, but you
>can access it at:
>
> 
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

>
>It hasn't been merged with release-4-5-patches in some time, so many
>resolved bugs won't be fixed.
>
>-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
>
>
>--gmx-users mailing list gmx-users@gromacs.org 


> >
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> >.

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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] Questions about GB parameters

[Mark Abraham]

On 15/06/2011 4:24 AM, Justin A. Lemkul wrote:


Hi All,

I wanted to dig up an old discussion that hit the list a long time ago 
because I'm now encountering some problems understanding the GB 
settings myself.  The discussion in question is here:


http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html

I wanted to post a couple of questions based on Per's response.

1. Based on that post, it seems to me that the value in the gbr column 
should have a dielectric offset added to it during the GB 
calculations.  In the code, though (genborn.c, around line 484 in the 
latest release-4-5-patches), it looks like the dielectric offset is 
subtracted, not added.  I guess the code is reversing the process, 
going from GB radius back to vdW radius by subtracting the dielectric 
offset?  It seems, then, that the parameters in gbsa.itp should 
specify GB radii, not vdW radii, though the manual says the gbr column 
is "atomic van der Waals radii, which are used in computing the Born 
radii."  Is the opposite actually true?


It does look to me as though something is mis-sense here. The quantity 
given in gb_dielectric_offset is always subtracted from a value that I 
think is found in the gbr column of [implicit_genborn_parameters].


Mark

2. I am still unclear on the source of the HCT scaling factors.  From 
the reference cited in the manual, it would seem that scaling factors 
are interaction-dependent, at least when H atoms are concerned.  I 
also cannot find any indication of where these values came from.  None 
of the values of Table 2 in the HCT reference match the contents of 
the "hct" column.  Again I wonder if I'm missing something obvious :)


Thanks for any insight!

-Justin



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Re: [gmx-users] Water Potential Energy

[Mark Abraham]

On 15/06/2011 4:55 AM, Rini Gupta wrote:

Dear Mark,

Thanks for the reply!

I am using the same NPT conditions except time constants.
The simulation was performed at constant temperature (300K)
and pressure(1 bar) using velocity rescaling algorithm (tau=0.1 ps)
for temperature coupling and Berendsen coupling
scheme (tau=1 ps) for pressure coupling whereas the in the references 
the system was coupled to bath of constant temperature (300K) and 
pressure (1 bar) using time constants tau=0.4 ps for temperature 
coupling and taup=0.4 ps for pressure coupling.

Does it is making difference in calculated and reported values?


Maybe, but I'd randomly guess it would lead to a smaller difference than 
that.



I am using LINCS algorithm to keep the geometries of all the molecules
rigid. Other conditions are exactly same.

To see the size effect on the system,
I have also done the same calculations with 8000 molecules but result 
is same i.e. Water P.E=-46.7 kJ/mol.


I guess that means you are observing converged quantities. Maybe they 
weren't observing such?


There can also be differences in implementation between different codes 
such that absolute energies are not necessarily comparable. Energy 
differences should compare, however.


Mark


Please clarify this issue.

Best Regards,
Rini

On Tue, 14 Jun 2011 08:13:39 +0530 wrote
>On 14/06/2011 4:18 AM, Rini Gupta wrote:

> Dear gmx-users,

>

> I am using GROMACS 4.5.4 to run a pure water system using SPC/E model

> containing 32000 molecules. I have done the equilibration for 2 ns

> followed by production run of 5 ns using NPT ensemble at 300K.

> I am using PME for treating electrostatic interactions (cut-off 0.9 nm).

> My question is Potential Energy of the system I am getting is -46.7

> kJ/mol while literature value is -41.5 kJ/mol.

> Can anyone please tell me why this discrepancy is coming?



PE is size- and method-dependent. Are you reproducing the conditions

exactly?



Mark

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[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

[maria goranovic]

I am using the command:

trjcat -f *gro -o temp.xtc -cat

to concatenate about 40,000 frames of 14,000 atoms each. The commands works
well for 10,000 frames, but crashes for 40,000 frames after reading all the
frames. There is sufficient disk space. Is this a bug of some kind?

-- 
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Technical University of Denmark
Copenhagen
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Re: [gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

[Mark Abraham]

On 15/06/2011 10:58 PM, maria goranovic wrote:

I am using the command:

trjcat -f *gro -o temp.xtc -cat

to concatenate about 40,000 frames of 14,000 atoms each. The commands 
works well for 10,000 frames, but crashes for 40,000 frames after 
reading all the frames. There is sufficient disk space. Is this a bug 
of some kind?


Maybe you're running out of memory or running into a filesystem file 
size limit. Try doing things piece-wise.


Mark
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Re: [gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

[Justin A. Lemkul]

maria goranovic wrote:

I am using the command:

trjcat -f *gro -o temp.xtc -cat 

to concatenate about 40,000 frames of 14,000 atoms each. The commands 
works well for 10,000 frames, but crashes for 40,000 frames after 
reading all the frames. There is sufficient disk space. Is this a bug of 
some kind? 



Not a bug, but rather clunky code - trjcat consumes a huge amount of memory.  If 
your .gro files are large, then that is the likely limitation.  Convert the .gro 
frames to .xtc with trjconv, then concatenate those instead.


-Justin


--
Maria G.
Technical University of Denmark
Copenhagen



--


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] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

[maria goranovic]

thanks for the help .. will try

On Wed, Jun 15, 2011 at 3:02 PM, Justin A. Lemkul  wrote:

>
>
> maria goranovic wrote:
>
>> I am using the command:
>>
>> trjcat -f *gro -o temp.xtc -cat
>> to concatenate about 40,000 frames of 14,000 atoms each. The commands
>> works well for 10,000 frames, but crashes for 40,000 frames after reading
>> all the frames. There is sufficient disk space. Is this a bug of some kind?
>>
>
> Not a bug, but rather clunky code - trjcat consumes a huge amount of
> memory.  If your .gro files are large, then that is the likely limitation.
>  Convert the .gro frames to .xtc with trjconv, then concatenate those
> instead.
>
> -Justin
>
>
>  --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> 
>
> 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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Copenhagen
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[gmx-users] initial temperature ridiculously high

[GZ Zhang]

Hi, ALL

I met a bizarre in a NVT simulation in which the initial temperature is
ridiculously high.
Even though I specify the initial temperature to be 200 K.

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 200.0
gen_seed = 173529

Energies (kJ/mol)
   Bond   LJ (SR)Coulomb (SR)Coul.
recip.Potential
7.17894e+013.25101e+05 -3.75274e+05   - 3.13877e+05
-3.63978e+05
 Kinetic En.Total EnergyTemperature  Pressure (bar)
7.97000e+04   -2.84278e+05 1.7e+04  2.75198e+06

The force field I used is called CLAYFF(
http://www.sklogwiki.org/SklogWiki/index.php/CLAYFF_force_field),
in which all atoms except hydroxyl groups interact through non-bonded vdW
and electrostatic interactions.

What's more strange is that after 5 ps, the system converted from a ordered
layer structure
into a disordered structure, like melting, although temperature goes to 200
K.

Any comments?

Thanks in advance !

Guozhen
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Re: [gmx-users] initial temperature ridiculously high

[Justin A. Lemkul]

GZ Zhang wrote:

Hi, ALL

I met a bizarre in a NVT simulation in which the initial temperature is 
ridiculously high.

Even though I specify the initial temperature to be 200 K.

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 200.0
gen_seed = 173529

Energies (kJ/mol)
   Bond   LJ (SR)Coulomb (SR)Coul. 
recip.Potential
7.17894e+013.25101e+05 -3.75274e+05   - 3.13877e+05   
-3.63978e+05

 Kinetic En.Total EnergyTemperature  Pressure (bar)
7.97000e+04   -2.84278e+05 1.7e+04  2.75198e+06

The force field I used is called 
CLAYFF(http://www.sklogwiki.org/SklogWiki/index.php/CLAYFF_force_field), 
in which all atoms except hydroxyl groups interact through non-bonded 
vdW and electrostatic interactions.
  
What's more strange is that after 5 ps, the system converted from a 
ordered layer structure 
into a disordered structure, like melting, although temperature goes to 
200 K.


Any comments?



The combination of high temperature and really high pressure (beyond the normal 
+/- 1000 fluctuations) suggests that you have an unreasonable starting structure 
 and/or broken topology.  Atomic overlap (or bad parameters) will cause atoms 
to shoot wildly across the system, leading to large velocities and high 
temperature.  In this case, you were fortunate that the whole system didn't 
explode but somehow continued.


-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] Regarding H-bond autocorrelation

[bipin singh]

Thanks Sir,for your reply...
I have a silly question regarding the g_hbond's autocorrelation output:
The output contains the following four columns
(i)  Ac fin sys(t)
(ii)  Ac(t)
(iii) Cc contact,hb(t)
(iv) -dAc fs/dt

As I understood the first column is the acf with background
subtraction,and the second column is acf  without
background subtraction.Can you please refer some text from where I
could get the details about the above
mentioned output options and their importance in in H-bond dynamics.

On Tue, Jun 14, 2011 at 16:53, Erik Marklund  wrote:
> Could be. But, if memory serves me right, there's another dataset in the 
> output, which shows the acf without the "background subtraction".
>
> Erik
>
> 14 jun 2011 kl. 12.10 skrev bipin singh:
>
>> I am using the Gromacs 4.5.3is  that feature is present in
>> this version..
>>
>> On Mon, Jun 13, 2011 at 21:39, Erik Marklund  wrote:
>>> Hi,
>>>
>>> The problem is that g_hbond subtracts a "background level" to compensate 
>>> for the finite size of the system. I thought that feature had been taken 
>>> away, however. Are you using old code?
>>>
>>> Erik
>>>
>>> 12 jun 2011 kl. 19.33 skrev bipin singh:
>>>
 Hello,

 I am calculating the H-bond autocorrelation using g_hbond for my
 system, but after plotting
 I have observed that the value for c(t) is reaching to negative, as
 far as I know it can not be
 negative as the probability can not be negative...please suggest
 where is the problem..

 --
 ---
 Thanks and Regards,
 Bipin Singh
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>>>
>>> ---
>>> Erik Marklund, PhD student
>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>> phone:    +46 18 471 4537        fax: +46 18 511 755
>>> er...@xray.bmc.uu.se
>>> http://www2.icm.uu.se/molbio/elflab/index.html
>>>
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>>
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Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

[shivangi nangia]

Hello Justin and everybody,

I created a system of charged polyhistdine, counter anions and just 1 DHB
molecule is a box without making any change in the vdwradii.dat file.
This system does not energy minimize, it stops with the same message:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.

What can be done to fix this problem?


The part of  DHB itp file is:
[ moleculetype ]
; Name nrexcl
DHB  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OM 1  DHB OAA 1   -0.567  15.9994
 2 C 1  DHB CAH 11.135  12.0110
 3OM 1  DHB OAD 1   -0.568  15.9994
 4 C 1  DHB CAK 2   -0.004  12.0110
 5   CR1 1  DHB CAG 20.004  12.0110
 6HC 1  DHB HAG 20.033   1.0080
 7 C 1  DHB CAI 20.141  12.0110
 8OA 1  DHB OAB 2   -0.179  15.9994
 9 H 1  DHB HAB 20.005   1.0080
10   CR1 1  DHB CAE 30.000  12.0110
11HC 1  DHB HAE 30.000   1.0080
12   CR1 1  DHB CAF 30.000  12.0110
13HC 1  DHB HAF 30.000   1.0080
14 C 1  DHB CAJ 40.082  12.0110
15OA 1  DHB OAC 4   -0.113  15.9994
16 H 1  DHB HAC 40.031   1.0080





If I have the water/methanol or water:methanol in the system as the solvent,
the system runs fine.

Please help.

Thanks,
SN






On Tue, Jun 14, 2011 at 3:13 PM, Justin A. Lemkul  wrote:

>
>
> shivangi nangia wrote:
>
>> Dear Justin,
>>
>> I have run into another problem.
>>
>> I created the system by including DHB in vwdradii.dat as follows:
>>
>> ; Very approximate VanderWaals radii
>> ; only used for drawing atoms as balls or for calculating atomic overlap.
>> ; longest matches are used
>> ; '???' or '*' matches any residue name
>> ; 'AAA' matches any protein residue name
>> ???  C 0.15
>> ???  F 0.12
>> ???  H 0.04
>> ???  N 0.110
>> ???  O 0.105
>> ???  S 0.16
>> *DHB  C 0.5
>> DHB  H 0.5
>> DHB  O 0.5*
>> ; Water charge sites
>> SOL  MW0
>> SOL  LP0
>> ; Masses for vsite construction
>> GLY  MN1   0
>> GLY  MN2   0
>> ALA  MCB1  0
>> ALA  MCB2  0
>> VAL  MCG1  0
>> VAL  MCG2  0
>> ILE  MCG1  0
>> ILE  MCG2  0
>> ILE  MCD1  0
>> ILE  MCD2  0
>> LEU  MCD1  0
>> LEU  MCD2  0
>> MET  MCE1  0
>> MET  MCE2  0
>> TRP  MTRP1 0
>> TRP  MTRP2 0
>> THR  MCG1  0
>> THR  MCG2  0
>> LYSH MNZ1  0
>> LYSH MNZ2  0
>>
>> After making this change, DHB molecules were not over lapping with each
>> other.
>>
>> I tried to energy minimized the system.
>> minim.mdp
>> ; minim.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> integrator  = steep ; Algorithm (steep = steepest descent
>> minimization)
>> ;emtol= 1000.0; Stop minimization when the maximum force < 1000.0
>> kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps  = 5 ; Maximum number of (minimization) steps to
>> perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist = 1  ; Frequency to update the neighbor list and long
>> range forces
>> ns_type = grid  ; Method to determine neighbor list (simple, grid)
>> rlist= 1.0; Cut-off for making neighbor list (short range forces)
>> coulombtype = PME; Treatment of long range electrostatic interactions
>> rcoulomb = 1.0; Short-range electrostatic cut-off
>> rvdw = 1.0; Short-range Van der Waals cut-off
>> pbc  = xyz   ; Periodic Boundary Conditions (yes/no)
>> constraints = none
>>
>>
>>  After about 6000 steps the run stops with the message:
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 10
>>
>> Double precision normally gives you higher accuracy.
>>
>> Steepest Descents converged to machine precision in 6012 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  =  1.0655116e+05
>> Maximum force =  1.6512177e+02 on atom 2076
>> Norm of force =  6.5337501e+00
>>
>>
>>
>> The potential energy is high, but I still continued to equilibration.
>> After NVT equilibration, NVT equilbration runs into the following error as
>> soon it starts:
>>
>>
>> Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which is
>> larger than the 1-4 table size 2.000 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> /var/spool/pbs/mom_priv/jobs/1

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

[Justin A. Lemkul]

shivangi nangia wrote:

Hello Justin and everybody,

I created a system of charged polyhistdine, counter anions and just 1 
DHB molecule is a box without making any change in the vdwradii.dat file.

This system does not energy minimize, it stops with the same message:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.

What can be done to fix this problem?



Take some time to search the Gromacs website and the mailing list archive.  You 
would have undoubtedly found either this:


http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

or the hundreds of other messages that post this message, which is neither a 
problem, nor an error, per se.




The part of  DHB itp file is:
[ moleculetype ]
; Name nrexcl
DHB  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OM 1  DHB OAA 1   -0.567  15.9994
 2 C 1  DHB CAH 11.135  12.0110
 3OM 1  DHB OAD 1   -0.568  15.9994
 4 C 1  DHB CAK 2   -0.004  12.0110
 5   CR1 1  DHB CAG 20.004  12.0110
 6HC 1  DHB HAG 20.033   1.0080
 7 C 1  DHB CAI 20.141  12.0110
 8OA 1  DHB OAB 2   -0.179  15.9994
 9 H 1  DHB HAB 20.005   1.0080
10   CR1 1  DHB CAE 30.000  12.0110
11HC 1  DHB HAE 30.000   1.0080
12   CR1 1  DHB CAF 30.000  12.0110
13HC 1  DHB HAF 30.000   1.0080
14 C 1  DHB CAJ 40.082  12.0110
15OA 1  DHB OAC 4   -0.113  15.9994
16 H 1  DHB HAC 40.031   1.0080




This topology looks like complete junk.  Earlier I provided you a link to PRODRG 
tips and told you there was an article referenced there you should read.  I 
certainly hope you will do so.  If you run a simulation with a lousy topology, 
you'll get lousy results.  Either the system will be unstable or the results 
will be completely untrustworthy.






If I have the water/methanol or water:methanol in the system as the 
solvent, the system runs fine.




Well, what's the solvent in the case of the unstable system?  Just because some 
other systems appear stable does not mean anything else will be.


-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] centering a bilayer at a cartesian coordinate

[chris . neale]

Dear users:

I am trying to process a trajectory so that a group of molecules has  
their center of mass at a constant position in Cartesian space. I have  
not been able to figure out how to do this.


The reason that I would like this is that I have conducted umbrella  
sampling of a solute along the normal to a lipid bilayer and I would  
like to create a movie of a false-trajectory of the immersion profile.  
Such processing is also important for generating SDFs and for use with  
g_density.


I expect that the problems that I am having are due to volume  
fluctuations in the NPT ensemble.


The best idea that I have tried was (gromacs 4.5.3):

trjconv -center -box 10 10 15

where the original dimensions are much less that 10 10 15

But still, when I run g_traj on the processed .gro file I do not get  
similar values for the COM.


In more detail:

echo 0 | trjconv -s md1.tpr -f md1_50ps_md1.part0001.xtc -o tmp.xtc -e  
10 -pbc mol

# select POPC for centering and System for output and use a .tpr with pbc=no
echo -e "13\n0\n" | trjconv -s empty.tpr -f tmp.xtc -box 10 10 15  
-center -pbc none -o tmp2.xtc

# select POPC for coordinate output
echo 13 | g_traj  -s empty.tpr -f tmp2.xtc -ox -com -nopbc

 99550  4.8424  5.00025 7.49519
 99600  4.79691 4.94304 7.39868
 99650  4.75789 4.85189 7.41581
 99700  4.74974 4.80423 7.48257
 99750  5.07858 5.04788 7.51654
 99800  4.99091 4.78976 7.47778
 99850  5.11406 4.84656 7.48769
 99900  5.09739 5.12395 7.47889
 99950  5.0411  4.88659 7.52737
 10 4.91271 5.07101 7.50397

For Z, the value is 7.48037+/-0.072562 (MIN=7.3 and MAX=7.8)

If I look at the frames from the min and max z values, they do clearly  
differ in the placement of the bilayer along z.


###

To simplify things, I redid this while only using the phosphorous  
atoms (1 per lipid) in the centering and coordinate output.


Here, Z=7.49323+/-0.0658727 (MIN=7.3 and MAX=7.7)

To verify this and since all the atoms have the same mass, I checked  
it with awk:


echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 47550 -b 4 -o look_low.gro
echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 80750 -b 8 -o  
look_high.gro

cat look_low.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.39197
cat look_high.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.62207

###

Finally, I rechecked with a single atom and here it worked exactly as  
expected. The atoms is placed at 5 5 7.5 in every single frame.


###

Then I checked using 2 phosphorous atoms from the same (or,  
separately, different) leaflets, and the result was the same:


$ tail coord.xvg
 99550  5   5   7.5
 99600  5   5.0005  7.5
 99650  5.0005  5.0005  7.5005
 99700  5   5.0005  7.5
 99750  5.0005  5   7.5005
 99800  5   5.0005  7.5005
 99850  5   5   7.5005
 99900  5.0005  5   7.5005
 99950  5.0005  5   7.4995
 10 5   5   7.5


Then using 3 phosphorous atoms from (containing atoms from both  
leaflets), and now there is more deviation:


$ tail coord.xvg
 99550  5.48833 5.30233 6.972
 99600  5.48733 5.29233 6.97167
 99650  5.50033 5.29567 6.93467
 99700  5.52133 5.27433 6.93967
 99750  5.489   5.253   6.99133
 99800  5.481   5.319   6.91533
 99850  5.47867 5.309   6.827
 99900  5.48733 5.292   6.83133
 99950  5.52767 5.276.86867
 10 5.518   5.319   6.89167

(MIN=6.7 and MAX=7.1)

I originally had problems with pbc during trjconv in which the -center  
option would place the bilayer at the peripheries of the unit cell in  
some frames (COM should still be at the center). This is what lead me  
to the route that I have used above (a .tpr that was generated with  
pbc=no and trjconv -pbc none -center). Nevertheless, I think that  
perhaps trjconv is using pbc information even in this case where ti  
should not.


##

If anybody can see what I am doing wrong or has a method to center a  
bilayer at a cartesian coordinate, then I am very interested.


Thank you for your time,
Chris.


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[gmx-users] centering a bilayer at a cartesian coordinate

[chris . neale]

I solved it. It was my own error to assume that trjconv -center  
centers the COM. Actually, it centers the value of (min+max)/2 in each  
dimension.


I can modify trjconv locally to do what I want.

Thank you,
Chris.

static void center_x(int ecenter,rvec x[],matrix box,int n,int  
nc,atom_id ci[])

{
int i,m,ai;
rvec cmin,cmax,box_center,dx;

if (nc > 0) {
copy_rvec(x[ci[0]],cmin);
copy_rvec(x[ci[0]],cmax);
for(i=0; i cmax[m])
cmax[m]=x[ai][m];
}
}
calc_box_center(ecenter,box,box_center);
for(m=0; m
Dear users:

I am trying to process a trajectory so that a group of molecules has
their center of mass at a constant position in Cartesian space. I have
not been able to figure out how to do this.

The reason that I would like this is that I have conducted umbrella
sampling of a solute along the normal to a lipid bilayer and I would
like to create a movie of a false-trajectory of the immersion profile.
Such processing is also important for generating SDFs and for use with
g_density.

I expect that the problems that I am having are due to volume
fluctuations in the NPT ensemble.

The best idea that I have tried was (gromacs 4.5.3):

trjconv -center -box 10 10 15

where the original dimensions are much less that 10 10 15

But still, when I run g_traj on the processed .gro file I do not get
similar values for the COM.

In more detail:

echo 0 | trjconv -s md1.tpr -f md1_50ps_md1.part0001.xtc -o tmp.xtc -e
10 -pbc mol
# select POPC for centering and System for output and use a .tpr with pbc=no
echo -e "13\n0\n" | trjconv -s empty.tpr -f tmp.xtc -box 10 10 15
-center -pbc none -o tmp2.xtc
# select POPC for coordinate output
echo 13 | g_traj  -s empty.tpr -f tmp2.xtc -ox -com -nopbc

  99550 4.8424  5.00025 7.49519
  99600 4.79691 4.94304 7.39868
  99650 4.75789 4.85189 7.41581
  99700 4.74974 4.80423 7.48257
  99750 5.07858 5.04788 7.51654
  99800 4.99091 4.78976 7.47778
  99850 5.11406 4.84656 7.48769
  99900 5.09739 5.12395 7.47889
  99950 5.0411  4.88659 7.52737
  104.91271 5.07101 7.50397

For Z, the value is 7.48037+/-0.072562 (MIN=7.3 and MAX=7.8)

If I look at the frames from the min and max z values, they do clearly
differ in the placement of the bilayer along z.

###

To simplify things, I redid this while only using the phosphorous
atoms (1 per lipid) in the centering and coordinate output.

Here, Z=7.49323+/-0.0658727 (MIN=7.3 and MAX=7.7)

To verify this and since all the atoms have the same mass, I checked
it with awk:

echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 47550 -b 4 -o   
look_low.gro

echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 80750 -b 8 -o
look_high.gro
cat look_low.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.39197
cat look_high.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.62207

###

Finally, I rechecked with a single atom and here it worked exactly as
expected. The atoms is placed at 5 5 7.5 in every single frame.

###

Then I checked using 2 phosphorous atoms from the same (or,
separately, different) leaflets, and the result was the same:

$ tail coord.xvg
  99550 5   5   7.5
  99600 5   5.0005  7.5
  99650 5.0005  5.0005  7.5005
  99700 5   5.0005  7.5
  99750 5.0005  5   7.5005
  99800 5   5.0005  7.5005
  99850 5   5   7.5005
  99900 5.0005  5   7.5005
  99950 5.0005  5   7.4995
  105   5   7.5


Then using 3 phosphorous atoms from (containing atoms from both
leaflets), and now there is more deviation:

$ tail coord.xvg
  99550 5.48833 5.30233 6.972
  99600 5.48733 5.29233 6.97167
  99650 5.50033 5.29567 6.93467
  99700 5.52133 5.27433 6.93967
  99750 5.489   5.253   6.99133
  99800 5.481   5.319   6.91533
  99850 5.47867 5.309   6.827
  99900 5.48733 5.292   6.83133
  99950 5.52767 5.276.86867
  105.518   5.319   6.89167

(MIN=6.7 and MAX=7.1)

I originally had problems with pbc during trjconv in which the -center
option would place the bilayer at the peripheries of the unit cell in
some frames (COM should still be at the center). This is what lead me
to the route that I have used above (a .tpr that was generated with
pbc=no and trjconv -pbc none -center). Nevertheless, I think that
perhaps trjconv is using pbc information even in this case where ti
should not.

##

If anybody can see what I am doing wrong or has a method to center a
bilayer at a cartesian coordinate, then I am very interested.

Thank you for your time,
Chris.







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[gmx-users] CHARMM forcefield

[simon sham]

Hi,
I have two questions about using the charmm force field. 
1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl 
and fix_top_for_charmm.pl?
2. I got the following note when I tried to do energy minim. with grompp:

NOTE 1 [file topol.top]:
  The largest charge group contains 12 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Is this a problem?

Thanks for your insight!

Simon
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Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Amit Choubey]

Dear all,

Could anyone direct me to the manual for local pressure calculation or a
place where everything is mentioned about it ? I have been only able to
collect bits and pieces from the mailing lists.

Thank you
Amit

On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham wrote:

>  On 15/06/2011 9:09 PM, Jianguo Li wrote:
>
>  Dear all,
>
> I have made a test calculation of local pressure using version 4.5 for my
> membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives
> the localpressure data. Howeve, instead of giving an anveraged data of the
> local pressure, mdrun gives a separate file for each frame, so I got many
> files: localpressure.dat0, localpressure.dat1, localpressure.dat2,
> localpressure.dat3 ..
> Then I need to calculate the pressure tensor for each frame and make
> average. but these localpressure.dat files are very big (each file is about
> 30 Mb), occupying large space of the hard disk. Can anyone give some
> suggestions on how to fix this? Thank you very much!
>
>
> I would expect that the output frequency is configurable, but can only
> suggest you consult what documentation exists for this version. Your main
> alternatives are
>
> * to compress the files with (say) bzip2 or (less effective) gzip and
> construct a script to uncompress them singly and analyse them "on the fly"
> (AMBER users do a bit of this kind of thing, Google around)
> * to discard ones that are too frequent. However, judging from the numbers
> below, every 100ps is probably OK.
>
> Mark
>
>
>  The command is:
> mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
> box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1
> And the output message is:
> 
> Dumping local pressure based on 1 frames to localpressure.dat0...
> Reading frame   2 time 119400.000
>
> Dumping local pressure based on 1 frames to localpressure.dat1...
> Reading frame   3 time 119500.000
>
> Dumping local pressure based on 1 frames to localpressure.dat2...
> Reading frame   4 time 119600.000
>
> Dumping local pressure based on 1 frames to localpressure.dat3...
> Reading frame   5 time 119700.000
>
> Dumping local pressure based on 1 frames to localpressure.dat4...
> Reading frame   6 time 119800.000
> ...
>
> Cheers,
> Jianguo
>
>
>
>  --
> *From:* Justin A. Lemkul  
> *To:* Discussion list for GROMACS users 
> 
> *Sent:* Friday, 10 June 2011 07:10:35
> *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5
>
>
>
> Amit Choubey wrote:
> > Thanks Justin, I tried to install the recent git version but the
> configure file is missing. How should I install this version ?
> >
>
> Run the bootstrap script.  It generates the configure script.
>
> -Justin
>
> >
> > On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul  jalem...@vt.edu>> wrote:
> >
> >
> >
> >Amit Choubey wrote:
> >
> >Dear all,
> >
> >I saw an unanswered post at
> >
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
> >
> >It is about calculating local pressure in v 4.5 when using
> >CHARMM FF. Could someone give me some pointers about this?
> >
> >
> >I don't know what the development status of version 4.5 is, but you
> >can access it at:
> >
> >
> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
> >
> >It hasn't been merged with release-4-5-patches in some time, so many
> >resolved bugs won't be fixed.
> >
> >-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
> >
> >
> >--gmx-users mailing listgmx-users@gromacs.org
> >
> >http://lists.gromacs.org/mailman/listinfo/gmx-users
> >Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
> >
>
> -- 
>
> 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/Support/Mailing_Lists/Search before posting!
> 

Re: [gmx-users] CHARMM forcefield

[Justin A. Lemkul]

simon sham wrote:

Hi,
I have two questions about using the charmm force field.
1. Do we still need to use the two perl scripts, convert_charmm_ 
to_gromacs.pl and fix_top_for_charmm.pl?


No.


2. I got the following note when I tried to do energy minim. with grompp:

NOTE 1 [file topol.top]:
  The largest charge group contains 12 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Is this a problem?



Yes.  CHARMM topologies should not use charge groups.  You should invoke pdb2gmx 
with the -nochargegrp option to create a proper topology.


-Justin


Thanks for your insight!

Simon



--


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] local pressure calcuation for Gromacs-4.5

[Justin A. Lemkul]

Amit Choubey wrote:

Dear all,

Could anyone direct me to the manual for local pressure calculation or a 
place where everything is mentioned about it ? I have been only able to 
collect bits and pieces from the mailing lists.




That's probably all there is to be found.  There's no manual linked from the git 
web interface or the ftp site.


-Justin


Thank you
Amit

On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham > wrote:


On 15/06/2011 9:09 PM, Jianguo Li wrote:

Dear all,

I have made a test calculation of local pressure using version 4.5
for my membrane simulation using CHARMM FF. When rerun the
simulation, mdrun gives the localpressure data. Howeve, instead of
giving an anveraged data of the local pressure, mdrun gives a
separate file for each frame, so I got many files:
localpressure.dat0, localpressure.dat1, localpressure.dat2,
localpressure.dat3 ..
Then I need to calculate the pressure tensor for each frame and
make average. but these localpressure.dat files are very big (each
file is about 30 Mb), occupying large space of the hard disk. Can
anyone give some suggestions on how to fix this? Thank you very much!


I would expect that the output frequency is configurable, but can
only suggest you consult what documentation exists for this version.
Your main alternatives are

* to compress the files with (say) bzip2 or (less effective) gzip
and construct a script to uncompress them singly and analyse them
"on the fly" (AMBER users do a bit of this kind of thing, Google around)
* to discard ones that are too frequent. However, judging from the
numbers below, every 100ps is probably OK.

Mark



The command is:
mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1
And the output message is:

Dumping local pressure based on 1 frames to localpressure.dat0...
Reading frame   2 time 119400.000  


Dumping local pressure based on 1 frames to localpressure.dat1...
Reading frame   3 time 119500.000  


Dumping local pressure based on 1 frames to localpressure.dat2...
Reading frame   4 time 119600.000  


Dumping local pressure based on 1 frames to localpressure.dat3...
Reading frame   5 time 119700.000  


Dumping local pressure based on 1 frames to localpressure.dat4...
Reading frame   6 time 119800.000  
...


Cheers,
Jianguo




*From:* Justin A. Lemkul  
*To:* Discussion list for GROMACS users 

*Sent:* Friday, 10 June 2011 07:10:35
*Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5



Amit Choubey wrote:
> Thanks Justin, I tried to install the recent git version but the
configure file is missing. How should I install this version ?
>

Run the bootstrap script.  It generates the configure script.

-Justin

>
> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul
mailto:jalem...@vt.edu> >> wrote:
>
>
>
>Amit Choubey wrote:
>
>Dear all,
>
>I saw an unanswered post at
>   
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html

>
>It is about calculating local pressure in v 4.5 when using
>CHARMM FF. Could someone give me some pointers about this?
>
>
>I don't know what the development status of version 4.5 is,
but you
>can access it at:
>
>   
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

>
>It hasn't been merged with release-4-5-patches in some time,
so many
>resolved bugs won't be fixed.
>
>-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
>
>
>--gmx-users mailing listgmx-users@gromacs.org

>>
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/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

[gmx-users] Including quadrupole-charge interaction in GROMACS

[WU Yanbin]

Dear GMXers,

Is there a way in GROMACS to include quadrupole-charge interaction?
Or is there a standard to way to mimic quadrupole moment using partial
charge?

Thank you.

Best,
Yanbin
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[gmx-users] g_density

[chris . neale]

Dear Matthias:

Did you run trjconv -center -pbc mol at some point before running  
g_density? With pbc, there are multiple ways to put the center of a  
system at the center of the box. This can lead to having the water  
slab in the center of the unit cell and the bilayer on the top and  
bottom z.


Without seeing the commands and the output, it is hard to say any more.

Chris.

-- original message --

Hi,

I have aligned a trajectory to a reference structure and have now run
g_density on both the original and the aligned trajectory in order to
find the bilayer headgroup position and the bilayer thickness.

g_density works fine with the original trajectory but there seems to
be a bug when running it to the aligned structure (Alignment done
using trjconv -fit progressive).

The density is calculated along the z direction (-d Z). The density
for positive z is calculated correctly, but the density for negative z
is shifted about 15nm to to the top end of the box size, as if the
density distribution along the z-axis were discontinuous.

Other then stitching the data together by hands, are there any obvious
better solutions?

Thanks,

Matthias

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[gmx-users] Position restraints

[Tom Dupree]

Greetings all,

I have run into a little bit of a problem.

I am trying to simulate a hetro-dimer. Through previous work we have identified 
302  C-alphas (of 960 odd residues) that don't move much. Previously we 
position restrained these atoms in our simulations using charmm which gave us a 
significant speed up in simulation time. My supervisor is keen for me to do a 
comparison of that method with a completely unrestrained system using the 53A6 
FF. I managed to generate a position restraint file using the .gro file and 
genrestr.
However when I get to the simulation step I can't get grompp to work.

I ran

genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr

As I understand my situation grompp is looking for atom numbers in subset.itp 
and matching them to the atom numbers in topol_Protein_chain_x.itp and since 
the atom numbers in subset.itp are based on the em.gro file it fails/goes out 
of range. 

Thanks to some chain breaks in my structure I have 6 chains instead of 2, is 
there a way convert the .gro numbers into the .itp numbers? and hence generate 
my restraint files based on the topol_Protein_chain_x.itp files?  Furthermore 
can I actually do a constraint matrix over multiple molecules?

Or is there a better way of achieving my desired result? (302 atoms across 2 
(6) chains constrained in their relative positions) 


All the best,

Tom


Fatal error:
[ file subset.itp, line 145 ]:
Atom index (5222) in constraints out of bounds (1-5149).
This probably means that you have inserted topology section "constraints"
in a part belonging to a different molecule than you intended to.
In that case move the "constraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

My topology file
;
;   File 'topol.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Tue May 31 11:44:23 2011
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx - VERSION 4.5.3
;
;   Command line was:
;   pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v 
;
;   Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif
#include "topol_Protein_chain_A2.itp"
#ifdef POSRES
#include "posre_Protein_chain_A2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B2.itp"
#ifdef POSRES
#include "posre_Protein_chain_B2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B3.itp"
#ifdef POSRES
#include "posre_Protein_chain_B3.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B4.itp"
#ifdef POSRES
#include "posre_Protein_chain_B4.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
___


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