Re: [gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95

[Floris Buelens]

Hi Fabricio,

It's not correct to change your value of alpha, you should use a single value 
for the whole transformation. The soft core potential is constructed so that 
the end points at lambda=0 and 1 represent the 'native' states (with no 
influence from the soft core parameters), and that intermediate values produce 
a smooth transformation. 
Best,

Floris



From: Ragnarok sdf 
To: gmx-users@gromacs.org
Sent: Monday, 10 August, 2009 20:54:35
Subject: [gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95

I have tried using the soft core correction for values of lambda above
0.5, because i read that the overlaping starts usually at this lambda
value. The problem is that now I values of deltaG where lambda is near
0.5 a little bit off-scale. What I mean is that what used to be a nice
sequencial decrease in values from lambda 0 to lambda 1, now gives me
a crazy value for lambda 0.5 (by crazy I mean 3 times larger) then for
lambda 0.55, 0.6, 0.65 etc, I get values 3 times smaller than what
they used to be. I guess that maybe using soft core correction for
lambda values starting from 0.5 was a little bit to soon. But then for
which lambda values should I start using soft core and how would I
justify my choice?
Thank you
Fabrício Bracht
- Ocultar texto das mensagens anteriores -

> I agree with Carsten. See perhaps the discussion at www.alchemistry.org as
> well.
>
> On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner  wrote:
>
>> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
>>
>>  I am performing FEP do obtain the dimerization of a protein in
>>> membrane. The lambda intervals i am using are 0.05 for each window.
>>> After that I rerun each lambda .trr perturbing the system (plus)0.05
>>> and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
>>> for each delta lambda.
>>> Well, I have encountered a problem when trying to simulate the last
>>> window (1.0 - 0.95 ). The simulation runs for a while and then dies.
>>> The log file says
>>> Step 2200  Warning: Pressure scaling more than 1%.
>>>
>>>  Hi Fabricio,
>>
>> do you use soft-core? If not, I think you need to, at least for
>> the intervals next to 0 and 1 to avoid singularities (these
>> can result in undefined / NaN forces). See chap. 4.5.1 and
>> 7.3.23 in the manual.
>>
>> Carsten
>>
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Re: [gmx-users] Re: itp file

[Vitaly V. Chaban]

Jamie,

I asked you to show the order of sections ([defaults], [atomtypes],
etc) as they go one after another after you added all the .itp files.

Now you gave me only the .top file file and I don't see what you have
in the itp.'s. Please make a list of sections like [defaults],
[atomtypes], [bonds], etc with respect to your .itp and look at the
sequence. Something will not be correct here.

Vitaly

On Tue, Aug 11, 2009 at 12:46 AM, Jamie Seyed wrote:
> Dear Vitaly,
> topol.top: -
> #include "ffoplsaa.itp"
> #include "spce.itp"
> #include "c80ch3.itp"
> [system]
> fullerene in water
> [molecules]
> C80CH3   1
> SOL   1000
> 
> my command is:
> grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
>
> Thank you for helping me out to solve the problem/ Regards/Jamie
>
>
> On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban 
> wrote:
>>
>> Jamie,
>>
>> The idea is the same. Some directive is not at its place. I cannot say
>> which is exactly because I don't see all the picture with your
>> topology file (+included files). Write the sequence of directives as
>> they go in .top (+included .itp) and then we will see what sections
>> must be shifted or maybe just swapped.
>>
>> Vitaly
>>
>> On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed
>> wrote:
>> > Hi Vitaly,
>> > When I add it back, I got the old error
>> > ---
>> > Program grompp, Version 4.0.5
>> > Source Code file: topio.c, line: 415
>> > Fatal error:
>> > Syntax error-File ffoplsaa.itp, line 18
>> > last line read:
>> > '[defaults]'
>> > Invalid order for directive defaults
>> > ---
>> > Now do you have any idea??? I appreciate your help/Jamie
>> >
>> > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed 
>> > wrote:
>> >>
>> >> Hi Vitaly,
>> >> I did it because I read from
>> >>
>> >> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>> >> that says:
>> >> "One solution is to simply comment out (or delete) the lines of code
>> >> out
>> >> in the file where it is included for the second time i.e., ..". So if
>> >> it is
>> >> the case I am going to undo it to see what happens... I will let you
>> >> know.
>> >> Thanks/Jamie
>> >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban 
>> >> wrote:
>> >>>
>> >>> Why did you comment out [defaults] in ffoplsaa.itp? The general idea
>> >>> is that the sections in the resulting topology file (after including
>> >>> #include's) must be placed in the strict order.
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Re: [gmx-users] Help with Testset

[Mark Abraham]

b95203...@ntu.edu.tw wrote:

Hi,
I have installed Gromacs without error, however, the testset result in:

FAILED. Check files in rb1
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED

I do not worry about the dec+water, since it is explained in the 
testset, but I don't know what to do about rb1. No output is found.

What should I do??


The test set is currently getting an overhaul. The simple/rb1 test is 
flawed, as I mentioned on gmx-developers yesterday. IIRC, I found 
versions 3.3.3 and 3.3.2 would fail simple/rb1, but 4.0.5 would pass it 
even with the flaw.


It is always a good idea to cite the version number you are using 
whenever discussing GROMACS, since there are known bugs and issues.


Mark
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[gmx-users] Help with Testset

[b95203004]

Hi,
I have installed Gromacs without error, however, the testset result in:

FAILED. Check files in rb1
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED

I do not worry about the dec+water, since it is explained in the  
testset, but I don't know what to do about rb1. No output is found.

What should I do??
It would be great if anyone can help me.
William

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Re: [gmx-users] Gromacs in Parallel

[TJ Piggot]

I agree. Mpich 1 is very old, you should try mpich 2 or lam or openmpi.

Tom

--On Tuesday, August 11, 2009 09:16:54 +1000 Mark Abraham 
 wrote:



Andrew Paluch wrote:

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote
process: 0 p2_21562: (302.964844) net_send: could not write to fd=5,
errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can
find, it seems as if this is a mpich issue and not an issue of Gromacs.
Has anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?


Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of
problems with particular MPI libraries, but you might try compiling
GROMACS with another such library. Whoever configured this machine should
probably look into the problem.

Mark
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--
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.

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RE: [gmx-users] Fatal Equilibration Errors

[Dallas B. Warren]

You might want to consider the parameters I developed for propylene
glycol  http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms of the parameterisation of ethylene glycol.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Jamie Seyed wrote:

Dear  Justin,
Thanks for your all valuable comments. Actually I got these 2 notes:
---

NOTE 1 [file topol.top, line unknown]:
  The largest charge group contains 24 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.

NOTE 2 [file md.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.

-

How I can trust my results specially for first one?? Many Thanks/Jamie



You should define smaller charge groups.  The tip given in the note is useful.

As for note 2, never use cut-off for electrostatics.  It is not as reliable as 
PME.

-Justin




On Mon, Aug 10, 2009 at 9:18 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

The gro file:
-
GROtesk MACabre and Sinister
 1836
   12C1   1.311   1.563   0.994
   12C2   1.220   1.635   1.079
   12C3   1.092   1.565   1.081
   12C4   1.108   1.449   0.996
.

   12H  118   1.438   1.092   1.244
   12H  119   1.413   1.098   1.426
   12H  120   1.291   1.033   1.329
   2SOL OW  121   0.569   1.275   1.165
   2SOLHW1  122   0.476   1.268   1.128
   2SOLHW2  123   0.580   1.364   1.209

...

 572SOLHW2 1833   2.024   1.991   2.158
 573SOL OW 1834   2.290   2.286   2.382
 573SOLHW1 1835   2.320   2.214   2.320
 573SOLHW2 1836   2.251   2.246   2.465
  2.64467   2.64467   2.64467

-
 and itp-file:

-

; Include forcefield parameters

[ moleculetype ]
; Namenrexcl
C60CH3 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge  
mass  typeBchargeB  massB
1   opls_145  1  C60CH3  C  1  0
12.011   ; qtot 0
2   opls_516  1  C60CH3  C  2  0
12.011   ; qtot 0

.

 
  71787969 3  1.74e+02  5.00e+00

 3.00e+00  1.74e+02  5.00e+00  3.00e+00
  697980 2 3  2.58e+02  5.00e+00
 3.00e+00  2.58e+02  5.00e+00  3.00e+00

[ system ]
; Name
C60CH3

[ molecules ]
; Compound#mols
C60CH3 1
---

Oh Ok now I understand that I should remove only one of the
[molecule]


The [ system ] and [ molecules ] directives *only* belong in the
system .top, never in an .itp file.  Remove both [ system ] and [
molecules ] from the .itp, and list the appropriate molecules in the
[ molecules ] directive of the .top only.

-Justin

sections in itp-file (right)??

Thanks a lot/ Please let me know if still something is
missing.../Thanks/Jamie


 On Mon, Aug 10, 2009 at 8:42 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Jamie Seyed wrote:

   First I put 1000, but after editconf and genbox it has been
   changed to 572. I only have 1 part with SOL 572...


   I'm thoroughly confused.  There is no need to manually manipulate
   these sections if you're allowing genbox, genion, etc to
manipulate
   them for you.  Please post the following information to get a
   resolution:

   1. Your .top file
   2. Your molecule.itp file (you can delete out lines in the atoms,
   bonds, dihedrals section so the file is not unnecessarily
long - I'm
   really just interested in the other directives that may be
present)

   -Justin

   On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Jamie Seyed wrote:

The gro file:
-
GROtesk MACabre and Sinister
 1836
12C1   1.311   1.563   0.994
12C2   1.220   1.635   1.079
12C3   1.092   1.565   1.081
12C4   1.108   1.449   0.996
.

12H  118   1.438   1.092   1.244
12H  119   1.413   1.098   1.426
12H  120   1.291   1.033   1.329
2SOL OW  121   0.569   1.275   1.165
2SOLHW1  122   0.476   1.268   1.128
2SOLHW2  123   0.580   1.364   1.209

...

  572SOLHW2 1833   2.024   1.991   2.158
  573SOL OW 1834   2.290   2.286   2.382
  573SOLHW1 1835   2.320   2.214   2.320
  573SOLHW2 1836   2.251   2.246   2.465
   2.64467   2.64467   2.64467

-
 and itp-file:

-

; Include forcefield parameters

[ moleculetype ]
; Namenrexcl
C60CH3 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1   opls_145  1  C60CH3  C  1  0 
12.011   ; qtot 0
 2   opls_516  1  C60CH3  C  2  0 
12.011   ; qtot 0

.

 

   71787969 3  1.74e+02  5.00e+00  3.00e+00  
1.74e+02  5.00e+00  3.00e+00
   697980 2 3  2.58e+02  5.00e+00  3.00e+00  
2.58e+02  5.00e+00  3.00e+00


[ system ]
; Name
C60CH3

[ molecules ]
; Compound#mols
C60CH3 1
---

Oh Ok now I understand that I should remove only one of the [molecule] 


The [ system ] and [ molecules ] directives *only* belong in the system .top, 
never in an .itp file.  Remove both [ system ] and [ molecules ] from the .itp, 
and list the appropriate molecules in the [ molecules ] directive of the .top only.


-Justin


sections in itp-file (right)??

Thanks a lot/ Please let me know if still something is 
missing.../Thanks/Jamie



 
On Mon, Aug 10, 2009 at 8:42 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

First I put 1000, but after editconf and genbox it has been
changed to 572. I only have 1 part with SOL 572...


I'm thoroughly confused.  There is no need to manually manipulate
these sections if you're allowing genbox, genion, etc to manipulate
them for you.  Please post the following information to get a
resolution:

1. Your .top file
2. Your molecule.itp file (you can delete out lines in the atoms,
bonds, dihedrals section so the file is not unnecessarily long - I'm
really just interested in the other directives that may be present)

-Justin

On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Jamie Seyed wrote:

   Hi Justin,

   Thanks again... . Actully I have a question: I have 1836
atoms
   (572 water and 1 molecule with 120 atoms). In top of my
file.gro
   I have 1836 and in topology in [molecules] I have c60ch3
1; and
   SOL 572 which means the same as above. So how I should
change it
   to get rid of error...??/


   The above should be correct.  However, you then have in your .top
   you posted earlier:


   [molecules]
   molecule   1
   SOL   1000

   This section is probably the source of your problem.  Again, as I
   said before, there should only ever be one [ molecules ]
section in
   the .top file.  Sounds like you've got two.

   -Justin

   Thank you in advance.../Jamie
   On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Jamie Seyed wrote:
First I put 1000, but after editconf and genbox it has been changed to 
572. I only have 1 part with SOL 572...




I'm thoroughly confused.  There is no need to manually manipulate these sections 
if you're allowing genbox, genion, etc to manipulate them for you.  Please post 
the following information to get a resolution:


1. Your .top file
2. Your molecule.itp file (you can delete out lines in the atoms, bonds, 
dihedrals section so the file is not unnecessarily long - I'm really just 
interested in the other directives that may be present)


-Justin

On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

Hi Justin,

Thanks again... . Actully I have a question: I have 1836 atoms
(572 water and 1 molecule with 120 atoms). In top of my file.gro
I have 1836 and in topology in [molecules] I have c60ch3 1; and
SOL 572 which means the same as above. So how I should change it
to get rid of error...??/


The above should be correct.  However, you then have in your .top
you posted earlier:


[molecules]
molecule   1
SOL   1000

This section is probably the source of your problem.  Again, as I
said before, there should only ever be one [ molecules ] section in
the .top file.  Sounds like you've got two.

-Justin

Thank you in advance.../Jamie
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Jamie Seyed wrote:

   Hi Justin,
   Oh yes. I had a line that include ff again and I deleted that
   (is that ok)? now I got a new error related to "number of
   coordinates in


   That's more than OK, that's correct.  As Mark pointed out, there
   should only ever be one invocation of [ defaults ] in a topology.


   coordinate file does not match topology..." I should fix this
   one now!!  


   Simple one to fix.  Figure out where the duplicate or missing
   molecules are within the topology.  I'm guessing your
molecule.itp
   was really a molecule.top, complete with [ defaults ], [
system ],
   and [ molecules ] directive, right? None of these should be
present
   in an .itp file, only a .top.

   -Justin

   Thanks a lot/Jamie


   On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   
 

Re: [gmx-users] Re: itp file

[Jamie Seyed]

First I put 1000, but after editconf and genbox it has been changed to 572.
I only have 1 part with SOL 572...

On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Thanks again... . Actully I have a question: I have 1836 atoms (572 water
>> and 1 molecule with 120 atoms). In top of my file.gro I have 1836 and in
>> topology in [molecules] I have c60ch3 1; and SOL 572 which means the same as
>> above. So how I should change it to get rid of error...??/
>>
>
> The above should be correct.  However, you then have in your .top you
> posted earlier:
>
> [molecules]
> molecule   1
> SOL   1000
>
> This section is probably the source of your problem.  Again, as I said
> before, there should only ever be one [ molecules ] section in the .top
> file.  Sounds like you've got two.
>
> -Justin
>
>  Thank you in advance.../Jamie
>> On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Jamie Seyed wrote:
>>
>>Hi Justin,
>>Oh yes. I had a line that include ff again and I deleted that
>>(is that ok)? now I got a new error related to "number of
>>coordinates in
>>
>>
>>That's more than OK, that's correct.  As Mark pointed out, there
>>should only ever be one invocation of [ defaults ] in a topology.
>>
>>
>>coordinate file does not match topology..." I should fix this
>>one now!!
>>
>>Simple one to fix.  Figure out where the duplicate or missing
>>molecules are within the topology.  I'm guessing your molecule.itp
>>was really a molecule.top, complete with [ defaults ], [ system ],
>>and [ molecules ] directive, right? None of these should be present
>>in an .itp file, only a .top.
>>
>>-Justin
>>
>>Thanks a lot/Jamie
>>
>>
>>On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>> >> wrote:
>>
>>
>>   Can you post the contents of molecule.itp?  The first
>>#include for
>>   the force field is likely not the problem; you've probably
>>#included
>>   it again in molecule.itp.
>>
>>   -Justin
>>
>>   Jamie Seyed wrote:
>>
>>   Dear all,
>>   I have a topology contains line as below. I do not
>> understand
>>   what is wrong with it that I get an error
>>   ---
>>Program grompp, Version 4.0.5
>>Source Code file: topio.c, line: 415
>>Fatal error:
>>Syntax error-File ffoplsaa.itp, line 18
>>last line read:
>>'[defaults]'
>>Invalid order for directive defaults
>>   --
>>   according to the page
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>>   I do not have twice default section... SO I do not know
>>exactly
>>   which files I should check... It says topology and ff.
>>Topology
>>   that I am using in grompp is as below and the
>>ffoplsaa.itp has
>>   only one default section...
>>   Would you please help me to solve the problem.
>>   topol.top: -
>>   #include "ffoplsaa.itp"
>>   #include "spce.itp"
>>   #include "molecule.itp"
>>   [system]
>>   fullerene in water
>>   [molecules]
>>   molecule   1
>>   SOL   1000
>>   
>>   Many Thanks in Advance and I appreciate your help/Jamie
>>
>>On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
>>   mailto:jamie.se...@gmail.com>
>>>
>>   > >>
>>   wrote:
>>
>>  Dear Vitaly,
>>  topol.top: -
>>  #include "ffoplsaa.itp"
>>  #include "spce.itp"
>>  #include "c80ch3.itp"
>>  [system]
>>  fullerene in water
>>  [molecules]
>>  C80CH3   1
>>  SOL   1000
>>  
>>  my command is:
>>  grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr
>> -maxwarn 10
>>  Thank you for helping me out to solve the problem/
>>   Regards/Jamie
>>  On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban
>>  mailto:vvcha...@gmail.com>
>>>
>>   

Re: [gmx-users] Re: itp file

[Mark Abraham]

Jamie Seyed wrote:

Hi Justin,
Thanks again... . Actully I have a question: I have 1836 atoms (572 water
and 1 molecule with 120 atoms). In top of my file.gro I have 1836 and in
topology in [molecules] I have c60ch3 1; and SOL 572 which means the same as
above. So how I should change it to get rid of error...??/ Thank you in
advance.../Jamie


Make sure you have only one [ molecules ] section. I think Justin's 
probably picked your problem, inasmuch as you've just renamed a 
molecule.top to molecule.itp without removing the directives that should 
not be in an .itp file.


Mark


On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul  wrote:



Jamie Seyed wrote:


Hi Justin,
Oh yes. I had a line that include ff again and I deleted that (is that
ok)? now I got a new error related to "number of coordinates in


That's more than OK, that's correct.  As Mark pointed out, there should
only ever be one invocation of [ defaults ] in a topology.

coordinate file does not match topology..." I should fix this one now!!
Simple one to fix.  Figure out where the duplicate or missing molecules are
within the topology.  I'm guessing your molecule.itp was really a
molecule.top, complete with [ defaults ], [ system ], and [ molecules ]
directive, right? None of these should be present in an .itp file, only a
.top.

-Justin

Thanks a lot/Jamie


On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul > wrote:


   Can you post the contents of molecule.itp?  The first #include for
   the force field is likely not the problem; you've probably #included
   it again in molecule.itp.

   -Justin

   Jamie Seyed wrote:

   Dear all,
   I have a topology contains line as below. I do not understand
   what is wrong with it that I get an error
   ---
Program grompp, Version 4.0.5
Source Code file: topio.c, line: 415
Fatal error:
Syntax error-File ffoplsaa.itp, line 18
last line read:
'[defaults]'
Invalid order for directive defaults
   --
   according to the page

http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
   I do not have twice default section... SO I do not know exactly
   which files I should check... It says topology and ff. Topology
   that I am using in grompp is as below and the ffoplsaa.itp has
   only one default section...
   Would you please help me to solve the problem.
   topol.top: -
   #include "ffoplsaa.itp"
   #include "spce.itp"
   #include "molecule.itp"
   [system]
   fullerene in water
   [molecules]
   molecule   1
   SOL   1000
   
   Many Thanks in Advance and I appreciate your help/Jamie

On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
   mailto:jamie.se...@gmail.com>
   >>
   wrote:

  Dear Vitaly,
  topol.top: -
  #include "ffoplsaa.itp"
  #include "spce.itp"
  #include "c80ch3.itp"
  [system]
  fullerene in water
  [molecules]
  C80CH3   1
  SOL   1000
  
  my command is:
  grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
  Thank you for helping me out to solve the problem/
   Regards/Jamie
  On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban
  mailto:vvcha...@gmail.com>
   >> wrote:

  Jamie,

  The idea is the same. Some directive is not at its place. I
  cannot say
  which is exactly because I don't see all the picture with
   your
  topology file (+included files). Write the sequence of
   directives as
  they go in .top (+included .itp) and then we will see
   what sections
  must be shifted or maybe just swapped.

  Vitaly

  On Tue, Aug 11, 2009 at 12:34 AM, Jamie
  Seyedmailto:jamie.se...@gmail.com> >> wrote:
   > Hi Vitaly,
   > When I add it back, I got the old error
   > ---
   > Program grompp, Version 4.0.5
   > Source Code file: topio.c, line: 415
   > Fatal error:
   > Syntax error-File ffoplsaa.itp, line 18
   > last line read:
   > '[defaults]'
   > Invalid order for directive defaults
   > ---
   > Now do you have any idea??? I appreciate your help/Jamie
   >
   > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
  mailto:jamie.se...@gmail.com>
   >>
   wrote:
   >>
 

Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Jamie Seyed wrote:

Hi Justin,
Thanks again... . Actully I have a question: I have 1836 atoms (572 
water and 1 molecule with 120 atoms). In top of my file.gro I have 1836 
and in topology in [molecules] I have c60ch3 1; and SOL 572 which means 
the same as above. So how I should change it to get rid of error...??/ 


The above should be correct.  However, you then have in your .top you posted 
earlier:


[molecules]
molecule   1
SOL   1000

This section is probably the source of your problem.  Again, as I said before, 
there should only ever be one [ molecules ] section in the .top file.  Sounds 
like you've got two.


-Justin


Thank you in advance.../Jamie
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

Hi Justin,
Oh yes. I had a line that include ff again and I deleted that
(is that ok)? now I got a new error related to "number of
coordinates in


That's more than OK, that's correct.  As Mark pointed out, there
should only ever be one invocation of [ defaults ] in a topology.


coordinate file does not match topology..." I should fix this
one now!!  



Simple one to fix.  Figure out where the duplicate or missing
molecules are within the topology.  I'm guessing your molecule.itp
was really a molecule.top, complete with [ defaults ], [ system ],
and [ molecules ] directive, right? None of these should be present
in an .itp file, only a .top.

-Justin

Thanks a lot/Jamie


On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   Can you post the contents of molecule.itp?  The first
#include for
   the force field is likely not the problem; you've probably
#included
   it again in molecule.itp.

   -Justin

   Jamie Seyed wrote:

   Dear all,
   I have a topology contains line as below. I do not understand
   what is wrong with it that I get an error
   ---
Program grompp, Version 4.0.5
Source Code file: topio.c, line: 415
Fatal error:
Syntax error-File ffoplsaa.itp, line 18
last line read:
'[defaults]'
Invalid order for directive defaults
   --
   according to the page
 
 http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file

   I do not have twice default section... SO I do not know
exactly
   which files I should check... It says topology and ff.
Topology
   that I am using in grompp is as below and the
ffoplsaa.itp has
   only one default section...
   Would you please help me to solve the problem.
   topol.top: -
   #include "ffoplsaa.itp"
   #include "spce.itp"
   #include "molecule.itp"
   [system]
   fullerene in water
   [molecules]
   molecule   1
   SOL   1000
   
   Many Thanks in Advance and I appreciate your help/Jamie

On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
   mailto:jamie.se...@gmail.com>
>
    
>
   

Re: [gmx-users] Re: itp file

[Jamie Seyed]

Hi Justin,
Thanks again... . Actully I have a question: I have 1836 atoms (572 water
and 1 molecule with 120 atoms). In top of my file.gro I have 1836 and in
topology in [molecules] I have c60ch3 1; and SOL 572 which means the same as
above. So how I should change it to get rid of error...??/ Thank you in
advance.../Jamie
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Oh yes. I had a line that include ff again and I deleted that (is that
>> ok)? now I got a new error related to "number of coordinates in
>>
>
> That's more than OK, that's correct.  As Mark pointed out, there should
> only ever be one invocation of [ defaults ] in a topology.
>
> coordinate file does not match topology..." I should fix this one now!!
>>
>
> Simple one to fix.  Figure out where the duplicate or missing molecules are
> within the topology.  I'm guessing your molecule.itp was really a
> molecule.top, complete with [ defaults ], [ system ], and [ molecules ]
> directive, right? None of these should be present in an .itp file, only a
> .top.
>
> -Justin
>
> Thanks a lot/Jamie
>>
>>
>> On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>Can you post the contents of molecule.itp?  The first #include for
>>the force field is likely not the problem; you've probably #included
>>it again in molecule.itp.
>>
>>-Justin
>>
>>Jamie Seyed wrote:
>>
>>Dear all,
>>I have a topology contains line as below. I do not understand
>>what is wrong with it that I get an error
>>---
>> Program grompp, Version 4.0.5
>> Source Code file: topio.c, line: 415
>> Fatal error:
>> Syntax error-File ffoplsaa.itp, line 18
>> last line read:
>> '[defaults]'
>> Invalid order for directive defaults
>>--
>>according to the page
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>>I do not have twice default section... SO I do not know exactly
>>which files I should check... It says topology and ff. Topology
>>that I am using in grompp is as below and the ffoplsaa.itp has
>>only one default section...
>>Would you please help me to solve the problem.
>>topol.top: -
>>#include "ffoplsaa.itp"
>>#include "spce.itp"
>>#include "molecule.itp"
>>[system]
>>fullerene in water
>>[molecules]
>>molecule   1
>>SOL   1000
>>
>>Many Thanks in Advance and I appreciate your help/Jamie
>>
>> On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
>>mailto:jamie.se...@gmail.com>
>>>>
>>wrote:
>>
>>   Dear Vitaly,
>>   topol.top: -
>>   #include "ffoplsaa.itp"
>>   #include "spce.itp"
>>   #include "c80ch3.itp"
>>   [system]
>>   fullerene in water
>>   [molecules]
>>   C80CH3   1
>>   SOL   1000
>>   
>>   my command is:
>>   grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
>>   Thank you for helping me out to solve the problem/
>>Regards/Jamie
>>   On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban
>>   mailto:vvcha...@gmail.com>
>>>> wrote:
>>
>>   Jamie,
>>
>>   The idea is the same. Some directive is not at its place. I
>>   cannot say
>>   which is exactly because I don't see all the picture with
>>your
>>   topology file (+included files). Write the sequence of
>>directives as
>>   they go in .top (+included .itp) and then we will see
>>what sections
>>   must be shifted or maybe just swapped.
>>
>>   Vitaly
>>
>>   On Tue, Aug 11, 2009 at 12:34 AM, Jamie
>>   Seyed> >>> wrote:
>>> Hi Vitaly,
>>> When I add it back, I got the old error
>>> ---
>>> Program grompp, Version 4.0.5
>>> Source Code file: topio.c, line: 415
>>> Fatal error:
>>> Syntax error-File ffoplsaa.itp, line 18
>>> last line read:
>>> '[defaults]'
>>> Invalid order for directive defaults
>>> ---
>>> Now do you have any idea??? I appreciate your help/Jamie
>>>
>>> On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
>>   mailto:jamie.se...@gmail.com>
>>

Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Jamie Seyed wrote:

Hi Justin,
Oh yes. I had a line that include ff again and I deleted that (is that 
ok)? now I got a new error related to "number of coordinates in 


That's more than OK, that's correct.  As Mark pointed out, there should only 
ever be one invocation of [ defaults ] in a topology.


coordinate file does not match topology..." I should fix this one now!!  


Simple one to fix.  Figure out where the duplicate or missing molecules are 
within the topology.  I'm guessing your molecule.itp was really a molecule.top, 
complete with [ defaults ], [ system ], and [ molecules ] directive, right? 
None of these should be present in an .itp file, only a .top.


-Justin


Thanks a lot/Jamie

On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul > wrote:



Can you post the contents of molecule.itp?  The first #include for
the force field is likely not the problem; you've probably #included
it again in molecule.itp.

-Justin

Jamie Seyed wrote:

Dear all,
I have a topology contains line as below. I do not understand
what is wrong with it that I get an error
---
 Program grompp, Version 4.0.5
 Source Code file: topio.c, line: 415
 Fatal error:
 Syntax error-File ffoplsaa.itp, line 18
 last line read:
 '[defaults]'
 Invalid order for directive defaults
--
according to the page

http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
I do not have twice default section... SO I do not know exactly
which files I should check... It says topology and ff. Topology
that I am using in grompp is as below and the ffoplsaa.itp has
only one default section...
Would you please help me to solve the problem.
topol.top: -
#include "ffoplsaa.itp"
#include "spce.itp"
#include "molecule.itp"
[system]
fullerene in water
[molecules]
molecule   1
SOL   1000

Many Thanks in Advance and I appreciate your help/Jamie

 On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
mailto:jamie.se...@gmail.com>
>>
wrote:

   Dear Vitaly,
   topol.top: -
   #include "ffoplsaa.itp"
   #include "spce.itp"
   #include "c80ch3.itp"
   [system]
   fullerene in water
   [molecules]
   C80CH3   1
   SOL   1000
   
   my command is:
   grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
   Thank you for helping me out to solve the problem/
Regards/Jamie
   On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban
   mailto:vvcha...@gmail.com>
>> wrote:

   Jamie,

   The idea is the same. Some directive is not at its place. I
   cannot say
   which is exactly because I don't see all the picture with
your
   topology file (+included files). Write the sequence of
directives as
   they go in .top (+included .itp) and then we will see
what sections
   must be shifted or maybe just swapped.

   Vitaly

   On Tue, Aug 11, 2009 at 12:34 AM, Jamie
   Seyedmailto:jamie.se...@gmail.com> >> wrote:
> Hi Vitaly,
> When I add it back, I got the old error
> ---
> Program grompp, Version 4.0.5
> Source Code file: topio.c, line: 415
> Fatal error:
> Syntax error-File ffoplsaa.itp, line 18
> last line read:
> '[defaults]'
> Invalid order for directive defaults
> ---
> Now do you have any idea??? I appreciate your help/Jamie
>
> On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
   mailto:jamie.se...@gmail.com>
>>
wrote:
>>
>> Hi Vitaly,
>> I did it because I read from
>>
 
 http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file

>> that says:
>> "One solution is to simply comment out (or delete)
the lines
   of code out
>> in the file where it is included for the second time
i.e.,
   ..". So if it is
>> the case I am going to undo it to see wha

Re: [gmx-users] Re: itp file

[Jamie Seyed]

Hi Justin,
Oh yes. I had a line that include ff again and I deleted that (is that ok)?
now I got a new error related to "number of coordinates in coordinate file
does not match topology..." I should fix this one now!!  Thanks a lot/Jamie

On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul  wrote:

>
> Can you post the contents of molecule.itp?  The first #include for the
> force field is likely not the problem; you've probably #included it again in
> molecule.itp.
>
> -Justin
>
> Jamie Seyed wrote:
>
>> Dear all,
>> I have a topology contains line as below. I do not understand what is
>> wrong with it that I get an error
>> ---
>>  Program grompp, Version 4.0.5
>>  Source Code file: topio.c, line: 415
>>  Fatal error:
>>  Syntax error-File ffoplsaa.itp, line 18
>>  last line read:
>>  '[defaults]'
>>  Invalid order for directive defaults
>> --
>> according to the page
>> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>> I do not have twice default section... SO I do not know exactly which
>> files I should check... It says topology and ff. Topology that I am using in
>> grompp is as below and the ffoplsaa.itp has only one default section...
>> Would you please help me to solve the problem.
>> topol.top: -
>> #include "ffoplsaa.itp"
>> #include "spce.itp"
>> #include "molecule.itp"
>> [system]
>> fullerene in water
>> [molecules]
>> molecule   1
>> SOL   1000
>> 
>> Many Thanks in Advance and I appreciate your help/Jamie
>>
>>  On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed > jamie.se...@gmail.com>> wrote:
>>
>>Dear Vitaly,
>>topol.top: -
>>#include "ffoplsaa.itp"
>>#include "spce.itp"
>>#include "c80ch3.itp"
>>[system]
>>fullerene in water
>>[molecules]
>>C80CH3   1
>>SOL   1000
>>
>>my command is:
>>grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
>>Thank you for helping me out to solve the problem/ Regards/Jamie
>>On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban
>>mailto:vvcha...@gmail.com>> wrote:
>>
>>Jamie,
>>
>>The idea is the same. Some directive is not at its place. I
>>cannot say
>>which is exactly because I don't see all the picture with your
>>topology file (+included files). Write the sequence of directives
>> as
>>they go in .top (+included .itp) and then we will see what sections
>>must be shifted or maybe just swapped.
>>
>>Vitaly
>>
>>On Tue, Aug 11, 2009 at 12:34 AM, Jamie
>>Seyedmailto:jamie.se...@gmail.com>> wrote:
>> > Hi Vitaly,
>> > When I add it back, I got the old error
>> > ---
>> > Program grompp, Version 4.0.5
>> > Source Code file: topio.c, line: 415
>> > Fatal error:
>> > Syntax error-File ffoplsaa.itp, line 18
>> > last line read:
>> > '[defaults]'
>> > Invalid order for directive defaults
>> > ---
>> > Now do you have any idea??? I appreciate your help/Jamie
>> >
>> > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
>>mailto:jamie.se...@gmail.com>> wrote:
>> >>
>> >> Hi Vitaly,
>> >> I did it because I read from
>> >>
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>> >> that says:
>> >> "One solution is to simply comment out (or delete) the lines
>>of code out
>> >> in the file where it is included for the second time i.e.,
>>..". So if it is
>> >> the case I am going to undo it to see what happens... I will
>>let you know.
>> >> Thanks/Jamie
>> >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban
>>mailto:vvcha...@gmail.com>>
>> >> wrote:
>> >>>
>> >>> Why did you comment out [defaults] in ffoplsaa.itp? The
>>general idea
>> >>> is that the sections in the resulting topology file (after
>>including
>> >>> #include's) must be placed in the strict order.
>>
>>
>>
>>
>> 
>>
>> ___
>> 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
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ==

Re: [gmx-users] Re: itp file

[Mark Abraham]

Jamie Seyed wrote:

Dear all,
I have a topology contains line as below. I do not understand what is wrong
with it that I get an error
---
 Program grompp, Version 4.0.5
 Source Code file: topio.c, line: 415
 Fatal error:
 Syntax error-File ffoplsaa.itp, line 18
 last line read:
 '[defaults]'
 Invalid order for directive defaults
--
according to the page
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
I do not have twice default section... 


grompp thinks you do. Check the contents of all the files you #include. 
See http://oldwiki.gromacs.org/index.php/include_file_mechanism for 
explanations. As explained on the link you provided, only your 
forcefield .itp file has any business using this directive.


Mark


SO I do not know exactly which files
I should check... It says topology and ff. Topology that I am using in
grompp is as below and the ffoplsaa.itp has only one default section...
Would you please help me to solve the problem.
 topol.top: -
#include "ffoplsaa.itp"
#include "spce.itp"
#include "molecule.itp"
[system]
fullerene in water
[molecules]
molecule   1
SOL   1000

Many Thanks in Advance and I appreciate your help/Jamie


On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed  wrote:


Dear Vitaly,
topol.top: -
#include "ffoplsaa.itp"
#include "spce.itp"
#include "c80ch3.itp"
[system]
fullerene in water
[molecules]
C80CH3   1
SOL   1000

my command is:
grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10

Thank you for helping me out to solve the problem/ Regards/Jamie


On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban wrote:


Jamie,

The idea is the same. Some directive is not at its place. I cannot say
which is exactly because I don't see all the picture with your
topology file (+included files). Write the sequence of directives as
they go in .top (+included .itp) and then we will see what sections
must be shifted or maybe just swapped.

Vitaly

On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed
wrote:

Hi Vitaly,

 > When I add it back, I got the old error

---
Program grompp, Version 4.0.5
Source Code file: topio.c, line: 415
Fatal error:
Syntax error-File ffoplsaa.itp, line 18
last line read:
'[defaults]'
Invalid order for directive defaults
---
Now do you have any idea??? I appreciate your help/Jamie

On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed 

wrote:

Hi Vitaly,
I did it because I read from


http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file

that says:
"One solution is to simply comment out (or delete) the lines of code

out

in the file where it is included for the second time i.e., ..". So if

it is

the case I am going to undo it to see what happens... I will let you

know.

Thanks/Jamie
On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban 
wrote:

Why did you comment out [defaults] in ffoplsaa.itp? The general idea
is that the sections in the resulting topology file (after including
#include's) must be placed in the strict order.







___
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Can you post the contents of molecule.itp?  The first #include for the force 
field is likely not the problem; you've probably #included it again in molecule.itp.


-Justin

Jamie Seyed wrote:

Dear all,
I have a topology contains line as below. I do not understand what is 
wrong with it that I get an error

---
 Program grompp, Version 4.0.5
 Source Code file: topio.c, line: 415
 Fatal error:
 Syntax error-File ffoplsaa.itp, line 18
 last line read:
 '[defaults]'
 Invalid order for directive defaults
--
according to the page 
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
I do not have twice default section... SO I do not know exactly which 
files I should check... It says topology and ff. Topology that I am 
using in grompp is as below and the ffoplsaa.itp has only one default 
section...

Would you please help me to solve the problem.
topol.top: -
#include "ffoplsaa.itp"
#include "spce.itp"
#include "molecule.itp"
[system]
fullerene in water
[molecules]
molecule   1
SOL   1000

Many Thanks in Advance and I appreciate your help/Jamie

 
On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed > wrote:


Dear Vitaly,
topol.top: -
#include "ffoplsaa.itp"
#include "spce.itp"
#include "c80ch3.itp"
[system]
fullerene in water
[molecules]
C80CH3   1
SOL   1000

my command is:
grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
 
Thank you for helping me out to solve the problem/ Regards/Jamie
 
 
On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban

mailto:vvcha...@gmail.com>> wrote:

Jamie,

The idea is the same. Some directive is not at its place. I
cannot say
which is exactly because I don't see all the picture with your
topology file (+included files). Write the sequence of directives as
they go in .top (+included .itp) and then we will see what sections
must be shifted or maybe just swapped.

Vitaly

On Tue, Aug 11, 2009 at 12:34 AM, Jamie
Seyedmailto:jamie.se...@gmail.com>> wrote:
 > Hi Vitaly,
 > When I add it back, I got the old error
 > ---
 > Program grompp, Version 4.0.5
 > Source Code file: topio.c, line: 415
 > Fatal error:
 > Syntax error-File ffoplsaa.itp, line 18
 > last line read:
 > '[defaults]'
 > Invalid order for directive defaults
 > ---
 > Now do you have any idea??? I appreciate your help/Jamie
 >
 > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
mailto:jamie.se...@gmail.com>> wrote:
 >>
 >> Hi Vitaly,
 >> I did it because I read from
 >>

http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
 >> that says:
 >> "One solution is to simply comment out (or delete) the lines
of code out
 >> in the file where it is included for the second time i.e.,
..". So if it is
 >> the case I am going to undo it to see what happens... I will
let you know.
 >> Thanks/Jamie
 >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban
mailto:vvcha...@gmail.com>>
 >> wrote:
 >>>
 >>> Why did you comment out [defaults] in ffoplsaa.itp? The
general idea
 >>> is that the sections in the resulting topology file (after
including
 >>> #include's) must be placed in the strict order.






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


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Re: [gmx-users] Re: itp file

[Jamie Seyed]

Dear all,
I have a topology contains line as below. I do not understand what is wrong
with it that I get an error
---
 Program grompp, Version 4.0.5
 Source Code file: topio.c, line: 415
 Fatal error:
 Syntax error-File ffoplsaa.itp, line 18
 last line read:
 '[defaults]'
 Invalid order for directive defaults
--
according to the page
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
I do not have twice default section... SO I do not know exactly which files
I should check... It says topology and ff. Topology that I am using in
grompp is as below and the ffoplsaa.itp has only one default section...
Would you please help me to solve the problem.
 topol.top: -
#include "ffoplsaa.itp"
#include "spce.itp"
#include "molecule.itp"
[system]
fullerene in water
[molecules]
molecule   1
SOL   1000

Many Thanks in Advance and I appreciate your help/Jamie


On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed  wrote:

> Dear Vitaly,
> topol.top: -
> #include "ffoplsaa.itp"
> #include "spce.itp"
> #include "c80ch3.itp"
> [system]
> fullerene in water
> [molecules]
> C80CH3   1
> SOL   1000
> 
> my command is:
> grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
>
> Thank you for helping me out to solve the problem/ Regards/Jamie
>
>
> On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban wrote:
>
>> Jamie,
>>
>> The idea is the same. Some directive is not at its place. I cannot say
>> which is exactly because I don't see all the picture with your
>> topology file (+included files). Write the sequence of directives as
>> they go in .top (+included .itp) and then we will see what sections
>> must be shifted or maybe just swapped.
>>
>> Vitaly
>>
>> On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed
>> wrote:
>> > Hi Vitaly,
>>  > When I add it back, I got the old error
>> > ---
>> > Program grompp, Version 4.0.5
>> > Source Code file: topio.c, line: 415
>> > Fatal error:
>> > Syntax error-File ffoplsaa.itp, line 18
>> > last line read:
>> > '[defaults]'
>> > Invalid order for directive defaults
>> > ---
>> > Now do you have any idea??? I appreciate your help/Jamie
>> >
>> > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed 
>> wrote:
>> >>
>> >> Hi Vitaly,
>> >> I did it because I read from
>> >>
>> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>> >> that says:
>> >> "One solution is to simply comment out (or delete) the lines of code
>> out
>> >> in the file where it is included for the second time i.e., ..". So if
>> it is
>> >> the case I am going to undo it to see what happens... I will let you
>> know.
>> >> Thanks/Jamie
>> >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban 
>> >> wrote:
>> >>>
>> >>> Why did you comment out [defaults] in ffoplsaa.itp? The general idea
>> >>> is that the sections in the resulting topology file (after including
>> >>> #include's) must be placed in the strict order.
>>
>
>
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Re: [gmx-users] Gromacs in Parallel

[Mark Abraham]

Andrew Paluch wrote:

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote process: 0
p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can find,
it seems as if this is a mpich issue and not an issue of Gromacs.  Has
anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?


Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of 
problems with particular MPI libraries, but you might try compiling 
GROMACS with another such library. Whoever configured this machine 
should probably look into the problem.


Mark
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Re: [gmx-users] water.pdb file

[Justin A. Lemkul]

sunny mishra wrote:

Hi Justin,

That sounds perfect to me. I think using the water.mdp file and
water.top file I can create my own water.gro file including any number
of molecules i guess.

I realized one more thing that I need to create my own protein.ssd
file from do_dssp program I guess,  because in the tutorial I was
given these files already but for my own protein I have to create one.
In the MARTINI tutorial they have provided me the seq2itp.pl script
which can convert my 1K4C.seq file to 1K4C.itp file but for that I
need 1K4C.ssd file. The command is as:

seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp

I don't know how to create 1K4C.ssd file now because when I try to
create it using do_dssp it asks me to generate the topol.tpr file and
I cannot generate that before simulation. Do you have any idea about
this?



The .ssd file is just a text file with codes for secondary structure elements. 
I can think of two ways to generate it:


1. You can use the standalone dssp executable on the starting .pdb file to 
generate an analysis of secondary structure.


2. If your .pdb file is from the RCSB, it probably contains HELIX and SHEET 
entries that you can use to determine the secondary structure.


After either (1) or (2) above, create the .ssd file yourself.  A little tedious, 
potentially a lot of typing, but I don't know how else to do it.


-Justin

-Justin


Sunny

On Mon, Aug 10, 2009 at 6:31 PM, Justin A. Lemkul wrote:


sunny mishra wrote:

Hi Justin,

Thanks for the expedient reply. In the MARTINI tutorial they have
provided two water.gro files one for lipids and the other for
proteins. Protein water molecule file consists of 10800 atoms of water
and the lipid has 400 atoms. So even if I simulate any protein
structure after converting that to CG, can I use the same water.gro
file for protein always?


I don't know about different water files based on the system; that seems a
bit arbitrary.  I'm referring to the one single water.gro file here:

http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html

If there are differences between using the water structure with proteins and
lipids, any changes are likely reflected in the force field, version 2.0 for
lipids, and version 2.1, which is the extension to proteins, if there is a
difference at all.  Any reasonable equilibrated box of water will probably
suffice; your equilibration will likely take care of any differences, if
they exist.

-Justin


Sunny
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--


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


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--


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


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Re: [gmx-users] water.pdb file

[sunny mishra]

Hi Justin,

That sounds perfect to me. I think using the water.mdp file and
water.top file I can create my own water.gro file including any number
of molecules i guess.

I realized one more thing that I need to create my own protein.ssd
file from do_dssp program I guess,  because in the tutorial I was
given these files already but for my own protein I have to create one.
In the MARTINI tutorial they have provided me the seq2itp.pl script
which can convert my 1K4C.seq file to 1K4C.itp file but for that I
need 1K4C.ssd file. The command is as:

seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp

I don't know how to create 1K4C.ssd file now because when I try to
create it using do_dssp it asks me to generate the topol.tpr file and
I cannot generate that before simulation. Do you have any idea about
this?

Sunny

On Mon, Aug 10, 2009 at 6:31 PM, Justin A. Lemkul wrote:
>
>
> sunny mishra wrote:
>>
>> Hi Justin,
>>
>> Thanks for the expedient reply. In the MARTINI tutorial they have
>> provided two water.gro files one for lipids and the other for
>> proteins. Protein water molecule file consists of 10800 atoms of water
>> and the lipid has 400 atoms. So even if I simulate any protein
>> structure after converting that to CG, can I use the same water.gro
>> file for protein always?
>>
>
> I don't know about different water files based on the system; that seems a
> bit arbitrary.  I'm referring to the one single water.gro file here:
>
> http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
>
> If there are differences between using the water structure with proteins and
> lipids, any changes are likely reflected in the force field, version 2.0 for
> lipids, and version 2.1, which is the extension to proteins, if there is a
> difference at all.  Any reasonable equilibrated box of water will probably
> suffice; your equilibration will likely take care of any differences, if
> they exist.
>
> -Justin
>
>> Sunny
>> ___
>> gmx-users mailing list    gmx-us...@gromacs.org
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>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Force Field Charge Parameters

[Justin A. Lemkul]

Nancy wrote:
The OPLS-AA force field is used for glucose and trehalose in conjunction 
with other force fields in the article by Sukit Leekumjorn and Amadeu K. 
Sum:


"Molecular Dynamics Study on the Stabilization of Dehydrated Lipid 
Bilayers with Glucose and Trehalose". J. Phys. Chem. B, 2008, 112 (34), 
pp 10732–10740


Are you suggesting that the authors used incorrect parameters?



Not at all.  As a matter of fact, I know them both and am familiar with their 
work.  They did a lot of work to determine that the behavior of their systems 
was consistent with reality, and that this particular force field combination 
was appropriate.


My advice to you is that you have to do your homework.  Whatever parameters you 
choose to use must be validated in light of experimental observables.  There are 
no absolute rules that any arbitrary combinations of parameters will work in 
some arbitrary system, or that any "automated" system is going to be right. 
People can get in trouble if they assume some black box is going to do correct 
work for them.


As I have said numerous times, you have to demonstrate to your audience that the 
physical model you have devised reflects reality.  This is no small task, but it 
can be done.


-Justin



On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul > wrote:




Nancy wrote:

Hello,

I have successfully minimised and equilibrated two systems, one
consisting of a single molecule of ethylene glycol
(1,2-ethanediol) in a water box, and the other is one molecule
of glycerol, also in a water box.  I am planning to proceed to
simulate other sugar alcohols (e.g. erythritol, arabitol,
mannitol, etc).  I used topolbuild 1.2 to generate topologies
for ethanediol and glycerol, and for the various atoms in these
molecules, I used charge values from methanol (the methanol
tutorial included with GROMACS), i.e. +0.398 for hydroxyl
hydrogens, -0.574 for oxygens, and +0.176 for the carbons.


As I told you before, the origin of these charges, in the absence of
some published validation of the parameters, is questionable at best.


Should I use these charge values for an arbitrary sugar alcohol,
or should I use the charge values specified in the article:

"OPLS All-Atom Force Field for Carbohydrates". Damm, W., A.
Frontera, J. Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput.
Chem. 18:1955–1970.


If you are using OPLS, probably yes.  But as I recall, you were
running simulations with GROMOS96.  If this is the case, then using
OPLS charges or other parameters is wholly inappropriate.  The
simple fact is, you must use charges from the parameter set you
intend to simulate, otherwise go through the laborious process of
deriving them yourself.


Also, are there programs that will automatically generate charge
values and other parameters for an arbitrary molecule?


There are several options, like the R.E.D. server or antechamber
(available from the Amber folks), but be advised that you should
always follow the methodology for whatever force field you're using.
 If it's GROMOS (like you've been using before), neither of these
approaches is necessary, and they may not give you correct
parameters.  Read the primary literature and base your decisions on
what you find.

-Justin

Thank you.

Nancy






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


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Re: [gmx-users] water.pdb file

[Justin A. Lemkul]

sunny mishra wrote:

Hi Justin,

Thanks for the expedient reply. In the MARTINI tutorial they have
provided two water.gro files one for lipids and the other for
proteins. Protein water molecule file consists of 10800 atoms of water
and the lipid has 400 atoms. So even if I simulate any protein
structure after converting that to CG, can I use the same water.gro
file for protein always?



I don't know about different water files based on the system; that seems a bit 
arbitrary.  I'm referring to the one single water.gro file here:


http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html

If there are differences between using the water structure with proteins and 
lipids, any changes are likely reflected in the force field, version 2.0 for 
lipids, and version 2.1, which is the extension to proteins, if there is a 
difference at all.  Any reasonable equilibrated box of water will probably 
suffice; your equilibration will likely take care of any differences, if they exist.


-Justin


Sunny
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--


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


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Re: [gmx-users] Force Field Charge Parameters

[Nancy]

The OPLS-AA force field is used for glucose and trehalose in conjunction
with other force fields in the article by Sukit Leekumjorn and Amadeu K.
Sum:

"Molecular Dynamics Study on the Stabilization of Dehydrated Lipid Bilayers
with Glucose and Trehalose". J. Phys. Chem. B, 2008, 112 (34), pp
10732–10740

Are you suggesting that the authors used incorrect parameters?


On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul  wrote:

>
>
> Nancy wrote:
>
>> Hello,
>>
>> I have successfully minimised and equilibrated two systems, one consisting
>> of a single molecule of ethylene glycol (1,2-ethanediol) in a water box, and
>> the other is one molecule of glycerol, also in a water box.  I am planning
>> to proceed to simulate other sugar alcohols (e.g. erythritol, arabitol,
>> mannitol, etc).  I used topolbuild 1.2 to generate topologies for ethanediol
>> and glycerol, and for the various atoms in these molecules, I used charge
>> values from methanol (the methanol tutorial included with GROMACS), i.e.
>> +0.398 for hydroxyl hydrogens, -0.574 for oxygens, and +0.176 for the
>> carbons.
>>
>>
> As I told you before, the origin of these charges, in the absence of some
> published validation of the parameters, is questionable at best.
>
>  Should I use these charge values for an arbitrary sugar alcohol, or should
>> I use the charge values specified in the article:
>>
>> "OPLS All-Atom Force Field for Carbohydrates". Damm, W., A. Frontera, J.
>> Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput. Chem. 18:1955–1970.
>>
>>
> If you are using OPLS, probably yes.  But as I recall, you were running
> simulations with GROMOS96.  If this is the case, then using OPLS charges or
> other parameters is wholly inappropriate.  The simple fact is, you must use
> charges from the parameter set you intend to simulate, otherwise go through
> the laborious process of deriving them yourself.
>
>  Also, are there programs that will automatically generate charge values
>> and other parameters for an arbitrary molecule?
>>
>>
> There are several options, like the R.E.D. server or antechamber (available
> from the Amber folks), but be advised that you should always follow the
> methodology for whatever force field you're using.  If it's GROMOS (like
> you've been using before), neither of these approaches is necessary, and
> they may not give you correct parameters.  Read the primary literature and
> base your decisions on what you find.
>
> -Justin
>
>  Thank you.
>>
>> Nancy
>>
>>
>>
>>
>> 
>>
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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Re: [gmx-users] Fatal Equilibration Errors

[Bruce D. Ray]

On Sunday, August 9, 2009 at 4:32:19 PM, Nancy  wrote:

> I obtained the ethylene glycol (1,2-ethanediol) structure from the URL:
>  http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb
> 
> I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF
> Chimera (http://www.cgl.ucsf.edu/chimera/).
> 
> I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the 
> topologies:
> 
> $ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir 
> .../topolbuild1_2_2/dat/gromacs -ff gmx53a6
> 
> which outputs the files:
> 
> ethanediol.gro
> ethanediol.log
> ethanediolMOL.mol2
> ethanediol.top
> ffethanediol.itp
> posreethanediol.itp
> 
> I modified the "ffethanediol.itp" file to read:
> 
> ===
> #define _FF_GROMOS96
> #define _FF_GROMOS53A6
> #define _FF_USER
> 
> [ defaults ]
> ;nbfunc comb-rule  gen-pairs fudgeLJ  fudgeQQ
>   1 1 no 1.0  1.0
> 
> #include "ffG53a6nb.itp"
> ===
> 
> The
lack of hydrogen bonds between the solute and solvent molecules was
> due
to the lack of charges in the generated topology file
"ethanediol.top". 
> So I changed the "atoms" section of the topology
file (the original topology
> file is at the end of this message), and
this causes hydrogen bonds between the
> solute and solvent in numbers
comparable to that between the solvent molecules.
> 
> ===
>  [ atoms ]
> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
> 1   CH2 1   EDO  C11   0.17600  14.02700   ;   
> 0.000
> 2OA 1   EDO  O11   -0.5740  15.99940   ;   
> 0.000
> 3H  1   EDO HO11   0.39800   1.00800   ;   
> 0.000
> 4   CH2 1   EDO  C22   0.17600  14.02700   ;   
> 0.000
> 5OA 1   EDO  O22   -0.5740  15.99940   ;   
> 0.000
> 6H  1   EDO HO22   0.39800   1.00800   ;   
> 0.000
> ; total molecule charge =   0.000
> ===
> 
> I
obtained the charge values from the methanol tutoral included with
Gromacs
>  (.../share/gromacs/tutor/methanol/methanol.itp).  I then
enlarge the box and solvate the molecule:

I used a mol2 file that I generated from a sy2 file downloaded from NCI by first
running the file through dos2unix then replacing the 0 in the residue number
column with 1 EDO so that I had both a correct residue number column with a
residue name column.  The NCI data was missing the residue name column.  I then
read the mol2 file that resulted into UCSF Chimera and used it to generate 
gasteiger
charges for ethylene glycol.  Chimera wrote the following mol2 file as a result:

@MOLECULE
EDO
10 9 1 0 0
SMALL
AMBER99


@ATOM
  1 O1  0.0.0. O.3   1 EDO-0.3940
  2 C1 -0.9400   -0.1600   -1.0400 C.3   1 EDO 0.0662
  3 C2 -1.74001.1400   -1.1400 C.3   1 EDO 0.0662
  4 O2 -2.52001.28000.0200 O.3   1 EDO-0.3940
  5 H1  0.5196   -0.80240.0879 H 1 EDO 0.2102
  6 H2 -1.5882   -0.9871   -0.8384 H 1 EDO 0.0588
  7 H3 -0.4343   -0.3499   -1.9636 H 1 EDO 0.0588
  8 H4 -2.37211.1133   -2.0029 H 1 EDO 0.0588
  9 H5 -1.06961.9696   -1.2252 H 1 EDO 0.0588
 10 H6 -3.02712.0935   -0.0316 H 1 EDO 0.2102
@BOND
 115 1
 212 1
 327 1
 426 1
 523 1
 639 1
 738 1
 834 1
 94   10 1
@SUBSTRUCTURE
 1 EDO 2 RESIDUE   4 A EDO 0 ROOT


I processed this with topolbuild 1.3 and generated topologies with gromacs
53a6 and with opls-aa as the force fields.  I am attaching the results to this
as the tarred and gzipped file, ethanediol.tgz   I note that the opls-aa atom
types selected by topolbuld 1.3 have characteristic atom type charges charges
of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens,
+0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the
carbons.  The comparison to the gasteiger charges Chimera assigned to these
atoms is interesting.  The opls-aa topology generated also assigns to the
O1-C1-C2-O2 dihedral the diol constants found as a special define in
ffoplsaabon.itp

{snipped}

> The ethylene glycol lacks explicit non-polar hydrogens; is that
normal for this type of system,
> force field (based on GROMOS96 53a6)
and SPC/E water model?

The 53a6 force field is a united atoms model force field and incorporates 
non-polar
hydrogens in the parameters of the carbons to which they are bound.  If you want
to treat the non-polar hydrogens 

[gmx-users] water.pdb file

[sunny mishra]

Hi Justin,

Thanks for the expedient reply. In the MARTINI tutorial they have
provided two water.gro files one for lipids and the other for
proteins. Protein water molecule file consists of 10800 atoms of water
and the lipid has 400 atoms. So even if I simulate any protein
structure after converting that to CG, can I use the same water.gro
file for protein always?

Sunny
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Re: [gmx-users] Force Field Charge Parameters

[Justin A. Lemkul]

Nancy wrote:

Hello,

I have successfully minimised and equilibrated two systems, one 
consisting of a single molecule of ethylene glycol (1,2-ethanediol) in a 
water box, and the other is one molecule of glycerol, also in a water 
box.  I am planning to proceed to simulate other sugar alcohols (e.g. 
erythritol, arabitol, mannitol, etc).  I used topolbuild 1.2 to generate 
topologies for ethanediol and glycerol, and for the various atoms in 
these molecules, I used charge values from methanol (the methanol 
tutorial included with GROMACS), i.e. +0.398 for hydroxyl hydrogens, 
-0.574 for oxygens, and +0.176 for the carbons.




As I told you before, the origin of these charges, in the absence of some 
published validation of the parameters, is questionable at best.


Should I use these charge values for an arbitrary sugar alcohol, or 
should I use the charge values specified in the article:


"OPLS All-Atom Force Field for Carbohydrates". Damm, W., A. Frontera, J. 
Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput. Chem. 18:1955–1970.




If you are using OPLS, probably yes.  But as I recall, you were running 
simulations with GROMOS96.  If this is the case, then using OPLS charges or 
other parameters is wholly inappropriate.  The simple fact is, you must use 
charges from the parameter set you intend to simulate, otherwise go through the 
laborious process of deriving them yourself.


Also, are there programs that will automatically generate charge values 
and other parameters for an arbitrary molecule?




There are several options, like the R.E.D. server or antechamber (available from 
the Amber folks), but be advised that you should always follow the methodology 
for whatever force field you're using.  If it's GROMOS (like you've been using 
before), neither of these approaches is necessary, and they may not give you 
correct parameters.  Read the primary literature and base your decisions on what 
you find.


-Justin


Thank you.

Nancy






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


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Re: [gmx-users] water.pdb file

[Justin A. Lemkul]

sunny mishra wrote:

Hi all,

Thanks for all the previous help. I am starting to run my protein
simulations after going through the MARTINI tutorial. In MARTINI
tutorials I was provided with some of the input files but they have
also taught that how to make your own input files when you run your
own protein simulation. I have a quick question that I know how to
make all GROMACS input files except the water molecule files. I don't
know how to create water.pdb file on my own.



There is a suitable water structure on the MARTINI site.  Since each particle 
represents four(?) water molecules, I don't think it would be trivial to create 
such a file on your own from an existing atomistic structure (or from scratch). 
 Probably best to use theirs.


-Justin


Suggestions will be highly appreciable.

Thanks,

Sunny
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--


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


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[gmx-users] Force Field Charge Parameters

[Nancy]

Hello,

I have successfully minimised and equilibrated two systems, one consisting
of a single molecule of ethylene glycol (1,2-ethanediol) in a water box, and
the other is one molecule of glycerol, also in a water box.  I am planning
to proceed to simulate other sugar alcohols (e.g. erythritol, arabitol,
mannitol, etc).  I used topolbuild 1.2 to generate topologies for ethanediol
and glycerol, and for the various atoms in these molecules, I used charge
values from methanol (the methanol tutorial included with GROMACS), i.e.
+0.398 for hydroxyl hydrogens, -0.574 for oxygens, and +0.176 for the
carbons.

Should I use these charge values for an arbitrary sugar alcohol, or should I
use the charge values specified in the article:

"OPLS All-Atom Force Field for Carbohydrates". Damm, W., A. Frontera, J.
Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput. Chem. 18:1955–1970.

Also, are there programs that will automatically generate charge values and
other parameters for an arbitrary molecule?

Thank you.

Nancy
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[gmx-users] water.pdb file

[sunny mishra]

Hi all,

Thanks for all the previous help. I am starting to run my protein
simulations after going through the MARTINI tutorial. In MARTINI
tutorials I was provided with some of the input files but they have
also taught that how to make your own input files when you run your
own protein simulation. I have a quick question that I know how to
make all GROMACS input files except the water molecule files. I don't
know how to create water.pdb file on my own.

Suggestions will be highly appreciable.

Thanks,

Sunny
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Re: [gmx-users] Re: itp file

[Vitaly V. Chaban]

Jamie,

The idea is the same. Some directive is not at its place. I cannot say
which is exactly because I don't see all the picture with your
topology file (+included files). Write the sequence of directives as
they go in .top (+included .itp) and then we will see what sections
must be shifted or maybe just swapped.

Vitaly

On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed wrote:
> Hi Vitaly,
> When I add it back, I got the old error
> ---
> Program grompp, Version 4.0.5
> Source Code file: topio.c, line: 415
> Fatal error:
> Syntax error-File ffoplsaa.itp, line 18
> last line read:
> '[defaults]'
> Invalid order for directive defaults
> ---
> Now do you have any idea??? I appreciate your help/Jamie
>
> On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed  wrote:
>>
>> Hi Vitaly,
>> I did it because I read from
>> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>> that says:
>> "One solution is to simply comment out (or delete) the lines of code out
>> in the file where it is included for the second time i.e., ..". So if it is
>> the case I am going to undo it to see what happens... I will let you know.
>> Thanks/Jamie
>> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban 
>> wrote:
>>>
>>> Why did you comment out [defaults] in ffoplsaa.itp? The general idea
>>> is that the sections in the resulting topology file (after including
>>> #include's) must be placed in the strict order.
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Re: [gmx-users] Fatal Equilibration Errors

[Nancy]

The structure in the original PDB file of ethylene glycol was in the gauche
conformation.  When I minimised the solvated system, the molecule remained
in the gauche conformation.  However, during equilibration of the system,
the conformation of the molecule changed to trans within less than one
picosecond.  It remained in the trans conformation for the rest of the
equilibration.


Thanks,
Nancy



On Sun, Aug 9, 2009 at 5:49 PM, Nagy, Peter I. wrote:

>
> Dear Nancy,
>
>   It was useful to find charges for the solute... I am not a GROMACS user,
> so I do not know what checks have to be done for a non-protein or non-DNA
> solute. Anyway, this case helped develop data management for a non-standard
> solute.
>   It is normal to use united atom model for CH, CH2 and CH3 in GROMACS. As
> far as the charges are concerned, it is always a matter of speculation.
> Nobody knows what charges are "correct". Only a quantum MD (for the whole
> system) helps, where you need not derive charges since you do not use
> empirical pair potentials. Charges of -0.574 and 0.398 for the OH atoms are
> reasonable, although somewhat larger absolute values could also be used.
> Nonetheless, they already triggered the solute-solvent H-bonds, which was
> the Nr. 1 problem.
>   I do not know what conformation you derived from the web. Was it
> ORIGINALLY trans or gauche? As I wrote, the experiment found only 12% trans
> in aqueous solution. Try to start the structure from the so-called tGg'
> conformation or some other gauche(you may find them e.g. in our papers
> JACS,1991, 113, 6719; 1992, 114, 4752 and a complete set of conformations in
> the paper of Cramer and Truhlar in the JACS about 1995, I do not have the
> reference handy). If the system stays in gauche, then the simulation has
> been short starting from trans and/or the OCCO torsion barrier is too high
> for equilibration. I would start from the tGg' and would conduct at least
> 500 ps long simulation, check if trans appears and what is the gauche/trans
> ratio. If you do not find a trans starting from gauche or no gauche starting
> from trans, then I would reduce the OCCO torisonal. Also check whether the
> intramolcular hydrogen bonds remain maintained in the gauche structures.
> Hopefully these above help.
>   The ratio is a sensitive problem, and could depend on the applied charge
> sets, too. Thus you may need to conduct a more complicated test finding
> combination(s) of charges and torsion parameters, which produce good
> results. Maybe there are different combinations working equally well. I did
> not meet this problem when I performed the free energy perturbation
> calculations via Monte Carlo simulations with rigid solute geometries.
>
> Best regards
> Peter Nagy
>
>
>
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Re: [gmx-users] Re: itp file

[Vitaly V. Chaban]

Why did you comment out [defaults] in ffoplsaa.itp? The general idea
is that the sections in the resulting topology file (after including
#include's) must be placed in the strict order.

On Mon, Aug 10, 2009 at 11:50 PM, Jamie Seyed wrote:
> Hi Vitaly,
> Thanks for your good comments. Yes I deleted that and I run the program but
> finally I found a line that said 26 inconsistent shifts
> So I tried to do everything again properly. Now I faced with several
> problems and to get rid of them:
> I put ff*.itp in the top line of topol.top, I commented out the line
> [defaults] in ffoplsaa.itp
> but now I have a new error that
> -
> Fatal error: syntax eror -File ffoplsaanb.itp, line 1
> last line read:
> '[atomtype]'
> Invalid order for directive atomtype
> 
> I did not mixed the ff and I put ff.itp on the top of my topology file...
> would you please let me know what is causing the problem?? I appreciate your
> help.../Jamie
>
> On Mon, Aug 10, 2009 at 4:29 PM, Vitaly V. Chaban 
> wrote:
>>
>> Dear Jamie,
>>
>> > 1) when I have my itp file and only I need a gro file (with velocities)
>> > how
>> > can I make it??
>> .gro can be made from .pdb with editconf. Also you will find useful
>> genbox and genconf for the related tasks. The velocities are not
>> needed to start MD run. They can be assigned automatically by mdrun
>> with "gen_vel" keyword in grompp.mdp.
>>
>> > 2) with Christopher Stiles method, why I got that fatal error and how I
>> > can
>> > solve it to run a correct md simulation??
>> What is the group BAL in your system? I guess you mentioned it in the
>> .mdp file, so the program looks for it and doesn't find anywhere.
>> Either delete it from .mdp or provide an information which atoms this
>> group contains (see "-n index.ndx").
>>
>> Good luck,
>>   Vitaly
>>
>> On Mon, Aug 10, 2009 at 9:53 PM, Jamie Seyed wrote:
>> > Dear Vitaly and all,
>> > I did copy my top file to a itp file and now for doing a md simulation I
>> > need a box of water and so I was thinking to make a .gro file and use
>> > editconf after that. But I did not know how, so I used the procedure by
>> > Christopher Stiles (I used editconf to make a gro file from pdb and I
>> > did
>> > not use my itp according to the procedure) the gro file doesn't
>> > contain
>> > velocities. Now when I run the grompp command, I got this Fatal error:
>> > Group BAL not found in indexfile
>> > my questions are
>> > 1) when I have my itp file and only I need a gro file (with velocities)
>> > how
>> > can I make it??
>> > 2) with Christopher Stiles method, why I got that fatal error and how I
>> > can
>> > solve it to run a correct md simulation??
>> > Many Thanks in advance/Jamie
>> >
>> > On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban 
>> > wrote:
>> >>
>> >> Jamie,
>> >>
>> >> The best solution is to copy all the sections ([atoms], [bonds], etc)
>> >> corresponding to each molecule into a separate file and then use
>> >> "include" statement like in C language to attach these .itp files to
>> >> .top file.
>> >>
>> >> So you will have only the numbers of the each kind of molecules in
>> >> your .top file. These manipulations are made only in the sake of
>> >> future comfort. Below is an example how I do it.
>> >>
>> >> Best,
>> >>   Vitaly
>> >>
>> >> ===topology  file==
>> >> #include "vvc.itp"
>> >> #include "15x15x50.itp"
>> >> #include "20x20x50.itp"
>> >> #include "25x25x50.itp"
>> >>
>> >>
>> >> [ system ]
>> >> MWCNT with LIBF4 solution
>> >>
>> >>
>> >> [ molecules ]
>> >> 15x15x50              1
>> >> 20x20x50              1
>> >> 25x25x50              1
>> >> LI+                          7
>> >> BF4                        7
>> >> Methanol           254
>> >>
>> >>
>> >> On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed
>> >> wrote:
>> >> > Dear Vitaly,
>> >> > Thanks for your reply. Justin helped me about that and I could get
>> >> > the
>> >> > topology by x2top. In your last email you said after that I can
>> >> > export
>> >> > it to
>> >> > the .itp right? Would you please explain more about that, I mean for
>> >> > example
>> >> > should I change it manually to be look like a itp file or is that
>> >> > something
>> >> > else?? I appreciate your help...
>> >> > Thanks a lot/Jamie
>> >> >
>> >> > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban
>> >> > 
>> >> > wrote:
>> >> >>
>> >> >> Jamie,
>> >> >>
>> >> >> What error messages do they provide? What force fields do you use?
>> >> >> There were many rumors about these utilities here in the list but
>> >> >> they
>> >> >> seem to be workable in most cases.
>> >> >>
>> >> >> Vitaly
>> >> >>
>> >> >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie Seyed
>> >> >> wrote:
>> >> >> > Hi Vitaly,
>> >> >> > Actually it doe's not work. I tried but I got error messages for
>> >> >> > both
>> >> >> > cases.
>> >> >> > Actually the structure is big and contains a c60 part. Do you have
>> >> >> > any
>> >> >> > a

Re: [gmx-users] Re: itp file

[Vitaly V. Chaban]

Dear Jamie,

> 1) when I have my itp file and only I need a gro file (with velocities) how
> can I make it??
.gro can be made from .pdb with editconf. Also you will find useful
genbox and genconf for the related tasks. The velocities are not
needed to start MD run. They can be assigned automatically by mdrun
with "gen_vel" keyword in grompp.mdp.

> 2) with Christopher Stiles method, why I got that fatal error and how I can
> solve it to run a correct md simulation??
What is the group BAL in your system? I guess you mentioned it in the
.mdp file, so the program looks for it and doesn't find anywhere.
Either delete it from .mdp or provide an information which atoms this
group contains (see "-n index.ndx").

Good luck,
   Vitaly

On Mon, Aug 10, 2009 at 9:53 PM, Jamie Seyed wrote:
> Dear Vitaly and all,
> I did copy my top file to a itp file and now for doing a md simulation I
> need a box of water and so I was thinking to make a .gro file and use
> editconf after that. But I did not know how, so I used the procedure by
> Christopher Stiles (I used editconf to make a gro file from pdb and I did
> not use my itp according to the procedure) the gro file doesn't contain
> velocities. Now when I run the grompp command, I got this Fatal error:
> Group BAL not found in indexfile
> my questions are
> 1) when I have my itp file and only I need a gro file (with velocities) how
> can I make it??
> 2) with Christopher Stiles method, why I got that fatal error and how I can
> solve it to run a correct md simulation??
> Many Thanks in advance/Jamie
>
> On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban 
> wrote:
>>
>> Jamie,
>>
>> The best solution is to copy all the sections ([atoms], [bonds], etc)
>> corresponding to each molecule into a separate file and then use
>> "include" statement like in C language to attach these .itp files to
>> .top file.
>>
>> So you will have only the numbers of the each kind of molecules in
>> your .top file. These manipulations are made only in the sake of
>> future comfort. Below is an example how I do it.
>>
>> Best,
>>   Vitaly
>>
>> ===topology  file==
>> #include "vvc.itp"
>> #include "15x15x50.itp"
>> #include "20x20x50.itp"
>> #include "25x25x50.itp"
>>
>>
>> [ system ]
>> MWCNT with LIBF4 solution
>>
>>
>> [ molecules ]
>> 15x15x50              1
>> 20x20x50              1
>> 25x25x50              1
>> LI+                          7
>> BF4                        7
>> Methanol           254
>>
>>
>> On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed wrote:
>> > Dear Vitaly,
>> > Thanks for your reply. Justin helped me about that and I could get the
>> > topology by x2top. In your last email you said after that I can export
>> > it to
>> > the .itp right? Would you please explain more about that, I mean for
>> > example
>> > should I change it manually to be look like a itp file or is that
>> > something
>> > else?? I appreciate your help...
>> > Thanks a lot/Jamie
>> >
>> > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban 
>> > wrote:
>> >>
>> >> Jamie,
>> >>
>> >> What error messages do they provide? What force fields do you use?
>> >> There were many rumors about these utilities here in the list but they
>> >> seem to be workable in most cases.
>> >>
>> >> Vitaly
>> >>
>> >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie Seyed
>> >> wrote:
>> >> > Hi Vitaly,
>> >> > Actually it doe's not work. I tried but I got error messages for both
>> >> > cases.
>> >> > Actually the structure is big and contains a c60 part. Do you have
>> >> > any
>> >> > advice? I could not find in the topology part of archive...
>> >> > Thanks/Jamie
>> >> >
>> >> >
>> >> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban 
>> >> > wrote:
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?
>> >> >> Sometimes also it appears easier to make the topology by hand if
>> >> >> your
>> >> >> structure is not big. Please see the topologies for some molecules
>> >> >> in
>> >> >> the gromacs archive to use them as an example.
>> >> >>
>> >> >> Vitaly
>> >> >>
>> >> >> >
>> >> >> > Dear gmx users,
>> >> >> > I need some help for generating a itp file for my molecular
>> >> >> > structure. I
>> >> >> > am
>> >> >> > using molden and now I have the xyz and pdb files. I read through
>> >> >> > mailing
>> >> >> > list but seems I should provide itp myself. But I don't know the
>> >> >> > right
>> >> >> > way
>> >> >> > to do that. Is it using molden and find one-by-one bond sand
>> >> >> > angles
>> >> >> > and
>> >> >> > dihedrals... . If I have already the itp file for a part of
>> >> >> > molecule
>> >> >> > is
>> >> >> > it
>> >> >> > only to add the information of new atoms to the old itp file?? I
>> >> >> > will
>> >> >> > really
>> >> >> > appreciate it if someone gives me better ideas and more related
>> >> >> > information
>> >> >> > to make my itp file.
>> >> >> >
>> >> >> > Many Thanks in Advance,
>> >> >> > Jamie
>> >> >> > -- ne

[gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95

[Ragnarok sdf]

I have tried using the soft core correction for values of lambda above
0.5, because i read that the overlaping starts usually at this lambda
value. The problem is that now I values of deltaG where lambda is near
0.5 a little bit off-scale. What I mean is that what used to be a nice
sequencial decrease in values from lambda 0 to lambda 1, now gives me
a crazy value for lambda 0.5 (by crazy I mean 3 times larger) then for
lambda 0.55, 0.6, 0.65 etc, I get values 3 times smaller than what
they used to be. I guess that maybe using soft core correction for
lambda values starting from 0.5 was a little bit to soon. But then for
which lambda values should I start using soft core and how would I
justify my choice?
Thank you
Fabrício Bracht
- Ocultar texto das mensagens anteriores -

> I agree with Carsten. See perhaps the discussion at www.alchemistry.org as
> well.
>
> On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner  wrote:
>
>> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
>>
>>  I am performing FEP do obtain the dimerization of a protein in
>>> membrane. The lambda intervals i am using are 0.05 for each window.
>>> After that I rerun each lambda .trr perturbing the system (plus)0.05
>>> and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
>>> for each delta lambda.
>>> Well, I have encountered a problem when trying to simulate the last
>>> window (1.0 - 0.95 ). The simulation runs for a while and then dies.
>>> The log file says
>>> Step 2200  Warning: Pressure scaling more than 1%.
>>>
>>>  Hi Fabricio,
>>
>> do you use soft-core? If not, I think you need to, at least for
>> the intervals next to 0 and 1 to avoid singularities (these
>> can result in undefined / NaN forces). See chap. 4.5.1 and
>> 7.3.23 in the manual.
>>
>> Carsten
>>
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[gmx-users] Re: gmx-users Digest, Vol 64, Issue 42

[Ragnarok sdf]

I have tried using the soft core correction for values of lambda above
0.5, because i read that the overlaping starts usually at this lambda
value. The problem is that now I values of deltaG where lambda is near
0.5 a little bit off-scale. What I mean is that what used to be a nice
sequencial decrease in values from lambda 0 to lambda 1, now gives me
a crazy value for lambda 0.5 (by crazy I mean 3 times larger) then for
lambda 0.55, 0.6, 0.65 etc, I get values 3 times smaller than what
they used to be. I guess that maybe using soft core correction for
lambda values starting from 0.5 was a little bit to soon. But then for
which lambda values should I start using soft core and how would I
justify my choice?
Thank you
Fabrício Bracht

> I agree with Carsten. See perhaps the discussion at www.alchemistry.org as
> well.
>
> On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner  wrote:
>
>> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
>>
>>  I am performing FEP do obtain the dimerization of a protein in
>>> membrane. The lambda intervals i am using are 0.05 for each window.
>>> After that I rerun each lambda .trr perturbing the system (plus)0.05
>>> and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
>>> for each delta lambda.
>>> Well, I have encountered a problem when trying to simulate the last
>>> window (1.0 - 0.95 ). The simulation runs for a while and then dies.
>>> The log file says
>>> Step 2200  Warning: Pressure scaling more than 1%.
>>>
>>>  Hi Fabricio,
>>
>> do you use soft-core? If not, I think you need to, at least for
>> the intervals next to 0 and 1 to avoid singularities (these
>> can result in undefined / NaN forces). See chap. 4.5.1 and
>> 7.3.23 in the manual.
>>
>> Carsten
>>
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Re: [gmx-users] Re: itp file

[Jamie Seyed]

Hi Justin,
Ok.Thanks for comments and advice, I appreciate.../Jamie

On Mon, Aug 10, 2009 at 3:06 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> Dear Vitaly and all,
>> I did copy my top file to a itp file and now for doing a md simulation I
>> need a box of water and so I was thinking to make a .gro file and use
>> editconf after that. But I did not know how, so I used the procedure by
>> Christopher Stiles (I used editconf to make a gro file from pdb and I did
>> not use my itp according to the procedure) the gro file doesn't contain
>> velocities. Now when I run the grompp command, I got this Fatal
>>
>
> The .gro file will not contain velocities until you have run dynamics.
>
> error:
>> Group BAL not found in indexfile
>>
>
> Then you have specified a molecule type that is not encompassed by your
> #included .itp files, or you have specified some special group in your .mdp
> file that doesn't exist without using a special index group.
>
> my questions are
>> 1) when I have my itp file and only I need a gro file (with velocities)
>> how can I make it??
>>
>
> I don't understand this question.
>
> 2) with Christopher Stiles method, why I got that fatal error and how I can
>> solve it to run a correct md simulation??
>>
>
> See above.  Without seeing the topology and .mdp file, it is hard to
> provide any more useful advice.
>
> I would seriously recommend running some simple tutorials on proteins (even
> if you don't care about proteins - these systems are very robust) to get a
> feel for procedures in Gromacs, how velocities are generated, how to use
> index files (if necessary), etc.
>
> -Justin
>
>  Many Thanks in advance/Jamie
>>
>>  On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban 
>> > vvcha...@gmail.com>> wrote:
>>
>>Jamie,
>>
>>The best solution is to copy all the sections ([atoms], [bonds], etc)
>>corresponding to each molecule into a separate file and then use
>>"include" statement like in C language to attach these .itp files to
>>.top file.
>>
>>So you will have only the numbers of the each kind of molecules in
>>your .top file. These manipulations are made only in the sake of
>>future comfort. Below is an example how I do it.
>>
>>Best,
>>  Vitaly
>>
>>===topology  file==
>>#include "vvc.itp"
>>#include "15x15x50.itp"
>>#include "20x20x50.itp"
>>#include "25x25x50.itp"
>>
>>
>>[ system ]
>>MWCNT with LIBF4 solution
>>
>>
>>[ molecules ]
>>15x15x50  1
>>20x20x50  1
>>25x25x50  1
>>LI+  7
>>BF47
>>Methanol   254
>>
>>
>>On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed>> wrote:
>> > Dear Vitaly,
>> > Thanks for your reply. Justin helped me about that and I could
>>get the
>> > topology by x2top. In your last email you said after that I can
>>export it to
>> > the .itp right? Would you please explain more about that, I mean
>>for example
>> > should I change it manually to be look like a itp file or is that
>>something
>> > else?? I appreciate your help...
>> > Thanks a lot/Jamie
>> >
>> > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban
>>mailto:vvcha...@gmail.com>>
>> > wrote:
>> >>
>> >> Jamie,
>> >>
>> >> What error messages do they provide? What force fields do you use?
>> >> There were many rumors about these utilities here in the list
>>but they
>> >> seem to be workable in most cases.
>> >>
>> >> Vitaly
>> >>
>> >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie
>>Seyedmailto:jamie.se...@gmail.com>> wrote:
>> >> > Hi Vitaly,
>> >> > Actually it doe's not work. I tried but I got error messages
>>for both
>> >> > cases.
>> >> > Actually the structure is big and contains a c60 part. Do you
>>have any
>> >> > advice? I could not find in the topology part of archive...
>> >> > Thanks/Jamie
>> >> >
>> >> >
>> >> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban
>>mailto:vvcha...@gmail.com>>
>>
>> >> > wrote:
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?
>> >> >> Sometimes also it appears easier to make the topology by hand
>>if your
>> >> >> structure is not big. Please see the topologies for some
>>molecules in
>> >> >> the gromacs archive to use them as an example.
>> >> >>
>> >> >> Vitaly
>> >> >>
>> >> >> >
>> >> >> > Dear gmx users,
>> >> >> > I need some help for generating a itp file for my molecular
>> >> >> > structure. I
>> >> >> > am
>> >> >> > using molden and now I have the xyz and pdb files. I read
>>through
>> >> >> > mailing
>> >> >> > list but seems I should provide itp myself. But I don't
>>know the
>> >> >> > ri

Re: [gmx-users] pairing error

[Justin A. Lemkul]

sahajmo...@gmail.com wrote:

So wat shud I do now I send u the attach files



Copy and paste the problematic section from your topology into an email so we 
can all see it.


-Justin



Regards,
Mohit Kumar

On 10-Aug-2009, at 12:05 PM, "Justin A. Lemkul"  wrote:




mohit kumar wrote:

im using dell core 2 duo with linux mint


OK, so what about showing us the topology?  That's probably a lot more 
relevant, anyway.


-Justin

--


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


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--


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


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Re: [gmx-users] pairing error

[sahajmohit]

So wat shud I do now I send u the attach files


Regards,
Mohit Kumar

On 10-Aug-2009, at 12:05 PM, "Justin A. Lemkul"  wrote:




mohit kumar wrote:

im using dell core 2 duo with linux mint


OK, so what about showing us the topology?  That's probably a lot  
more relevant, anyway.


-Justin

--


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


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Re: [gmx-users] Re: itp file

[Justin A. Lemkul]

Jamie Seyed wrote:

Dear Vitaly and all,
I did copy my top file to a itp file and now for doing a md simulation I 
need a box of water and so I was thinking to make a .gro file and use 
editconf after that. But I did not know how, so I used the procedure by 
Christopher Stiles (I used editconf to make a gro file from pdb and I 
did not use my itp according to the procedure) the gro file doesn't 
contain velocities. Now when I run the grompp command, I got this Fatal 


The .gro file will not contain velocities until you have run dynamics.


error:
Group BAL not found in indexfile


Then you have specified a molecule type that is not encompassed by your 
#included .itp files, or you have specified some special group in your .mdp file 
that doesn't exist without using a special index group.



my questions are
1) when I have my itp file and only I need a gro file (with velocities) 
how can I make it??


I don't understand this question.

2) with Christopher Stiles method, why I got that fatal error and how I 
can solve it to run a correct md simulation??


See above.  Without seeing the topology and .mdp file, it is hard to provide any 
more useful advice.


I would seriously recommend running some simple tutorials on proteins (even if 
you don't care about proteins - these systems are very robust) to get a feel for 
procedures in Gromacs, how velocities are generated, how to use index files (if 
necessary), etc.


-Justin


Many Thanks in advance/Jamie

On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban > wrote:


Jamie,

The best solution is to copy all the sections ([atoms], [bonds], etc)
corresponding to each molecule into a separate file and then use
"include" statement like in C language to attach these .itp files to
.top file.

So you will have only the numbers of the each kind of molecules in
your .top file. These manipulations are made only in the sake of
future comfort. Below is an example how I do it.

Best,
  Vitaly

===topology  file==
#include "vvc.itp"
#include "15x15x50.itp"
#include "20x20x50.itp"
#include "25x25x50.itp"


[ system ]
MWCNT with LIBF4 solution


[ molecules ]
15x15x50  1
20x20x50  1
25x25x50  1
LI+  7
BF47
Methanol   254


On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyedmailto:jamie.se...@gmail.com>> wrote:
 > Dear Vitaly,
 > Thanks for your reply. Justin helped me about that and I could
get the
 > topology by x2top. In your last email you said after that I can
export it to
 > the .itp right? Would you please explain more about that, I mean
for example
 > should I change it manually to be look like a itp file or is that
something
 > else?? I appreciate your help...
 > Thanks a lot/Jamie
 >
 > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban
mailto:vvcha...@gmail.com>>
 > wrote:
 >>
 >> Jamie,
 >>
 >> What error messages do they provide? What force fields do you use?
 >> There were many rumors about these utilities here in the list
but they
 >> seem to be workable in most cases.
 >>
 >> Vitaly
 >>
 >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie
Seyedmailto:jamie.se...@gmail.com>> wrote:
 >> > Hi Vitaly,
 >> > Actually it doe's not work. I tried but I got error messages
for both
 >> > cases.
 >> > Actually the structure is big and contains a c60 part. Do you
have any
 >> > advice? I could not find in the topology part of archive...
 >> > Thanks/Jamie
 >> >
 >> >
 >> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban
mailto:vvcha...@gmail.com>>
 >> > wrote:
 >> >>
 >> >> Hi,
 >> >>
 >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?
 >> >> Sometimes also it appears easier to make the topology by hand
if your
 >> >> structure is not big. Please see the topologies for some
molecules in
 >> >> the gromacs archive to use them as an example.
 >> >>
 >> >> Vitaly
 >> >>
 >> >> >
 >> >> > Dear gmx users,
 >> >> > I need some help for generating a itp file for my molecular
 >> >> > structure. I
 >> >> > am
 >> >> > using molden and now I have the xyz and pdb files. I read
through
 >> >> > mailing
 >> >> > list but seems I should provide itp myself. But I don't
know the
 >> >> > right
 >> >> > way
 >> >> > to do that. Is it using molden and find one-by-one bond
sand angles
 >> >> > and
 >> >> > dihedrals... . If I have already the itp file for a part of
molecule
 >> >> > is
 >> >> > it
 >> >> > only to add the information of new atoms to the old itp
file?? I will
 >> >> > really
 >> >> > appreciate it if someone gives me better idea

Re: [gmx-users] Re: itp file

[Jamie Seyed]

Dear Vitaly and all,
I did copy my top file to a itp file and now for doing a md simulation I
need a box of water and so I was thinking to make a .gro file and use
editconf after that. But I did not know how, so I used the procedure by
Christopher Stiles (I used editconf to make a gro file from pdb and I did
not use my itp according to the procedure) the gro file doesn't contain
velocities. Now when I run the grompp command, I got this Fatal error:
Group BAL not found in indexfile
my questions are
1) when I have my itp file and only I need a gro file (with velocities) how
can I make it??
2) with Christopher Stiles method, why I got that fatal error and how I can
solve it to run a correct md simulation??
Many Thanks in advance/Jamie

On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban wrote:

> Jamie,
>
> The best solution is to copy all the sections ([atoms], [bonds], etc)
> corresponding to each molecule into a separate file and then use
> "include" statement like in C language to attach these .itp files to
> .top file.
>
> So you will have only the numbers of the each kind of molecules in
> your .top file. These manipulations are made only in the sake of
> future comfort. Below is an example how I do it.
>
> Best,
>   Vitaly
>
> ===topology  file==
> #include "vvc.itp"
> #include "15x15x50.itp"
> #include "20x20x50.itp"
> #include "25x25x50.itp"
>
>
> [ system ]
> MWCNT with LIBF4 solution
>
>
> [ molecules ]
> 15x15x50  1
> 20x20x50  1
> 25x25x50  1
> LI+  7
> BF47
> Methanol   254
>
>
> On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed wrote:
> > Dear Vitaly,
> > Thanks for your reply. Justin helped me about that and I could get the
> > topology by x2top. In your last email you said after that I can export it
> to
> > the .itp right? Would you please explain more about that, I mean for
> example
> > should I change it manually to be look like a itp file or is that
> something
> > else?? I appreciate your help...
> > Thanks a lot/Jamie
> >
> > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban 
> > wrote:
> >>
> >> Jamie,
> >>
> >> What error messages do they provide? What force fields do you use?
> >> There were many rumors about these utilities here in the list but they
> >> seem to be workable in most cases.
> >>
> >> Vitaly
> >>
> >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie Seyed
> wrote:
> >> > Hi Vitaly,
> >> > Actually it doe's not work. I tried but I got error messages for both
> >> > cases.
> >> > Actually the structure is big and contains a c60 part. Do you have any
> >> > advice? I could not find in the topology part of archive...
> >> > Thanks/Jamie
> >> >
> >> >
> >> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban 
> >> > wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?
> >> >> Sometimes also it appears easier to make the topology by hand if your
> >> >> structure is not big. Please see the topologies for some molecules in
> >> >> the gromacs archive to use them as an example.
> >> >>
> >> >> Vitaly
> >> >>
> >> >> >
> >> >> > Dear gmx users,
> >> >> > I need some help for generating a itp file for my molecular
> >> >> > structure. I
> >> >> > am
> >> >> > using molden and now I have the xyz and pdb files. I read through
> >> >> > mailing
> >> >> > list but seems I should provide itp myself. But I don't know the
> >> >> > right
> >> >> > way
> >> >> > to do that. Is it using molden and find one-by-one bond sand angles
> >> >> > and
> >> >> > dihedrals... . If I have already the itp file for a part of
> molecule
> >> >> > is
> >> >> > it
> >> >> > only to add the information of new atoms to the old itp file?? I
> will
> >> >> > really
> >> >> > appreciate it if someone gives me better ideas and more related
> >> >> > information
> >> >> > to make my itp file.
> >> >> >
> >> >> > Many Thanks in Advance,
> >> >> > Jamie
> >> >> > -- next part --
> >> >> > An HTML attachment was scrubbed...
> >> >> > URL:
> >> >> >
> >> >> >
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090808/aaef0139/attachment-0001.html
> >> >> ___
> >> >> 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
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Vitaly V. Chaban, Ph.D. (ABD)
> >> School of Chemistry
> >> V.N. Karazin Kharkiv National University
> >> Svoboda sq.,4, Kharkiv 61077, Ukraine
> >> email: cha...@univer.kharkov.ua,vvcha...@gmail.com
> >> skype: vvchaban, cell.: +38-097-8259698
> >> http://www-rmn.univer.khark

Re: [gmx-users] GROMACS to AMBER

[Justin A. Lemkul]

Edson Fauth Vargas Filho wrote:

Hello all.
 
I would like to know if there is a way to convert .trr or .xtc files 
from GROMACS to .crd files (AMBER trajectory).
 


I once wrote a script that does the opposite (mdcrd -> xtc), so I imagine the 
opposite is possible, as well.  You can assemble a trajectory from sequential 
.pdb files as frames.  If you want to see the logic of what I did, the script is 
available at:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html

-Justin


Best regards,
Edson.




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


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Re: [gmx-users] pairing error

[Justin A. Lemkul]

mohit kumar wrote:

im using dell core 2 duo with linux mint


OK, so what about showing us the topology?  That's probably a lot more relevant, 
anyway.


-Justin

--


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


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[gmx-users] GROMACS to AMBER

[Edson Fauth Vargas Filho]

Hello all.

I would like to know if there is a way to convert .trr or .xtc files from
GROMACS to .crd files (AMBER trajectory).

Best regards,
Edson.
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Re: [gmx-users] pairing error

[mohit kumar]

im using dell core 2 duo with linux mint

On Mon, Aug 10, 2009 at 10:37 AM, Justin A. Lemkul  wrote:

>
>
> mohit kumar wrote:
>
>> still im getting problem, i checked the funct its have numerical
>> value..stilll getting problem..do i have to install gromac 3 version for
>> that..coz i having 4.0.5 version...
>>
>>
> Working with the most recent version (4.0.5) is always recommended.  The
> only reason to use an old version would be for consistency with older work.
>  Can you post your [ pairs ] section so we can have a look?  What type of
> machine are you using?  If it's Windows, then there may be problems with the
> file if it was edited using anything other than a plain text editor, in
> which case dos2unix is your friend.
>
> -Justin
>
>  On Thu, Aug 6, 2009 at 3:22 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>mohit kumar wrote:
>>
>>but i dnt find any 'type' column in my topology file..the grompp
>>programm with this top file works gud in 3.3 version..im having
>>4.0.5 version..is that can be issue?? shud i try in 3.3 version
>>
>>
>>This may be some new error-checking mechanism introduced in version
>>4.0.  In your topology, a function type for pairs should be defined,
>>according to the header of this section (from pdb2gmx):
>>
>>[ pairs ]
>>;  aiaj functc0c1c2
>>   c3
>>
>>If your "funct" column is blank or says "0" then that could be
>>giving the error.
>>
>>-Justin
>>
>>On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   mohit kumar wrote:
>>
>>   im running energy minimization for POPC bilayer but its
>>showing
>>   error which i cant figure out
>>
>>   -- ---
>>   Program grompp, VERSION 4.0.5
>>   Source code file: topdirs.c, line: 99
>>
>>   Fatal error:
>>   Invalid pairs type 0
>>
>>   what does this pair type mean and how can i solve it??
>>plz help me
>>
>>
>>   The error message is pretty clear.  Somewhere within the
>>topology,
>>   you have a "0" in the "type" column, which doesn't correspond
>>to any
>>   known pair type.
>>
>>   -Justin
>>
>>
>>
>>   MOHIT KUMAR
>>   Molecular Biochemistry & Biophysics
>>   Graduate Student
>>   Illinois Institute of Technology
>>   Chicago,IL, USA
>>
>>
>>
>> 
>>
>>   ___
>>   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
>>
>>
>>   --
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>231-9080
>>
>>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>   
>>   ___
>>   gmx-users mailing listgmx-users@gromacs.org
>>
>>   >
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at http://www.gromacs.org/searchbefore
>>   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
>>
>>
>>
>>
>>--MOHIT KUMAR
>>Molecular Biochemistry & Biophysics
>>Graduate Student
>>Illinois Institute

Re: [gmx-users] pairing error

[Justin A. Lemkul]

mohit kumar wrote:
still im getting problem, i checked the funct its have numerical 
value..stilll getting problem..do i have to install gromac 3 version for 
that..coz i having 4.0.5 version...




Working with the most recent version (4.0.5) is always recommended.  The only 
reason to use an old version would be for consistency with older work.  Can you 
post your [ pairs ] section so we can have a look?  What type of machine are you 
using?  If it's Windows, then there may be problems with the file if it was 
edited using anything other than a plain text editor, in which case dos2unix is 
your friend.


-Justin

On Thu, Aug 6, 2009 at 3:22 PM, Justin A. Lemkul > wrote:




mohit kumar wrote:

but i dnt find any 'type' column in my topology file..the grompp
programm with this top file works gud in 3.3 version..im having
4.0.5 version..is that can be issue?? shud i try in 3.3 version


This may be some new error-checking mechanism introduced in version
4.0.  In your topology, a function type for pairs should be defined,
according to the header of this section (from pdb2gmx):

[ pairs ]
;  aiaj functc0c1c2
   c3


If your "funct" column is blank or says "0" then that could be
giving the error.

-Justin

On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   mohit kumar wrote:

   im running energy minimization for POPC bilayer but its
showing
   error which i cant figure out

   -- ---
   Program grompp, VERSION 4.0.5
   Source code file: topdirs.c, line: 99

   Fatal error:
   Invalid pairs type 0

   what does this pair type mean and how can i solve it??
plz help me


   The error message is pretty clear.  Somewhere within the
topology,
   you have a "0" in the "type" column, which doesn't correspond
to any
   known pair type.

   -Justin



   MOHIT KUMAR
   Molecular Biochemistry & Biophysics
   Graduate Student
   Illinois Institute of Technology
   Chicago,IL, USA


 
 


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   --

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   
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-- 
MOHIT KUMAR

Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA


-- 



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

Re: [gmx-users] pairing error

[mohit kumar]

still im getting problem, i checked the funct its have numerical
value..stilll getting problem..do i have to install gromac 3 version for
that..coz i having 4.0.5 version...

On Thu, Aug 6, 2009 at 3:22 PM, Justin A. Lemkul  wrote:

>
>
> mohit kumar wrote:
>
>> but i dnt find any 'type' column in my topology file..the grompp programm
>> with this top file works gud in 3.3 version..im having 4.0.5 version..is
>> that can be issue?? shud i try in 3.3 version
>>
>>
> This may be some new error-checking mechanism introduced in version 4.0.
>  In your topology, a function type for pairs should be defined, according to
> the header of this section (from pdb2gmx):
>
> [ pairs ]
> ;  aiaj functc0c1c2c3
>
> If your "funct" column is blank or says "0" then that could be giving the
> error.
>
> -Justin
>
>  On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>mohit kumar wrote:
>>
>>im running energy minimization for POPC bilayer but its showing
>>error which i cant figure out
>>
>>-- ---
>>Program grompp, VERSION 4.0.5
>>Source code file: topdirs.c, line: 99
>>
>>Fatal error:
>>Invalid pairs type 0
>>
>>what does this pair type mean and how can i solve it?? plz help me
>>
>>
>>The error message is pretty clear.  Somewhere within the topology,
>>you have a "0" in the "type" column, which doesn't correspond to any
>>known pair type.
>>
>>-Justin
>>
>>
>>
>>MOHIT KUMAR
>>Molecular Biochemistry & Biophysics
>>Graduate Student
>>Illinois Institute of Technology
>>Chicago,IL, USA
>>
>>
>>
>>  
>>
>>___
>>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
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
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>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> MOHIT KUMAR
>> Molecular Biochemistry & Biophysics
>> Graduate Student
>> Illinois Institute of Technology
>> Chicago,IL, USA
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
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-- 
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
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[gmx-users] Gromacs in Parallel

[Andrew Paluch]

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote process: 0
p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can find,
it seems as if this is a mpich issue and not an issue of Gromacs.  Has
anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?

Thank you,

Andrew
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Re: [gmx-users] Re: itp file

[Vitaly V. Chaban]

Jamie,

The best solution is to copy all the sections ([atoms], [bonds], etc)
corresponding to each molecule into a separate file and then use
"include" statement like in C language to attach these .itp files to
.top file.

So you will have only the numbers of the each kind of molecules in
your .top file. These manipulations are made only in the sake of
future comfort. Below is an example how I do it.

Best,
   Vitaly

===topology  file==
#include "vvc.itp"
#include "15x15x50.itp"
#include "20x20x50.itp"
#include "25x25x50.itp"


[ system ]
MWCNT with LIBF4 solution


[ molecules ]
15x15x50  1
20x20x50  1
25x25x50  1
LI+  7
BF47
Methanol   254


On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed wrote:
> Dear Vitaly,
> Thanks for your reply. Justin helped me about that and I could get the
> topology by x2top. In your last email you said after that I can export it to
> the .itp right? Would you please explain more about that, I mean for example
> should I change it manually to be look like a itp file or is that something
> else?? I appreciate your help...
> Thanks a lot/Jamie
>
> On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban 
> wrote:
>>
>> Jamie,
>>
>> What error messages do they provide? What force fields do you use?
>> There were many rumors about these utilities here in the list but they
>> seem to be workable in most cases.
>>
>> Vitaly
>>
>> On Mon, Aug 10, 2009 at 1:39 AM, Jamie Seyed wrote:
>> > Hi Vitaly,
>> > Actually it doe's not work. I tried but I got error messages for both
>> > cases.
>> > Actually the structure is big and contains a c60 part. Do you have any
>> > advice? I could not find in the topology part of archive...
>> > Thanks/Jamie
>> >
>> >
>> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban 
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> Did you try pdb2gmx, x2top to make .top and then export to .itp?
>> >> Sometimes also it appears easier to make the topology by hand if your
>> >> structure is not big. Please see the topologies for some molecules in
>> >> the gromacs archive to use them as an example.
>> >>
>> >> Vitaly
>> >>
>> >> >
>> >> > Dear gmx users,
>> >> > I need some help for generating a itp file for my molecular
>> >> > structure. I
>> >> > am
>> >> > using molden and now I have the xyz and pdb files. I read through
>> >> > mailing
>> >> > list but seems I should provide itp myself. But I don't know the
>> >> > right
>> >> > way
>> >> > to do that. Is it using molden and find one-by-one bond sand angles
>> >> > and
>> >> > dihedrals... . If I have already the itp file for a part of molecule
>> >> > is
>> >> > it
>> >> > only to add the information of new atoms to the old itp file?? I will
>> >> > really
>> >> > appreciate it if someone gives me better ideas and more related
>> >> > information
>> >> > to make my itp file.
>> >> >
>> >> > Many Thanks in Advance,
>> >> > Jamie
>> >> > -- next part --
>> >> > An HTML attachment was scrubbed...
>> >> > URL:
>> >> >
>> >> > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090808/aaef0139/attachment-0001.html
>> >> ___
>> >> gmx-users mailing list    gmx-us...@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
>> >
>> >
>>
>>
>>
>> --
>> Vitaly V. Chaban, Ph.D. (ABD)
>> School of Chemistry
>> V.N. Karazin Kharkiv National University
>> Svoboda sq.,4, Kharkiv 61077, Ukraine
>> email: cha...@univer.kharkov.ua,vvcha...@gmail.com
>> skype: vvchaban, cell.: +38-097-8259698
>> http://www-rmn.univer.kharkov.ua/chaban.html
>> ===
>> !!! Looking for a postdoctoral position !!!
>> ===
>
>
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RE: [gmx-users] The pull rate of AFM

[Thomas Schlesier]

Hi, in GROMACS 3.3.x you must normalize the afm_dir1 vector by hand (or 
otherway around: afm_dir1 should be normalized).
Your vector is about 2.2 long -> so your pull-rate is 0.0022 -> and you see a 
much longer pulling distance (4nm against 2nm).
In GROMACS 4.0.x the vector is normalized automatically.
Hope this helps.
Thomas





Dear all, 

   First, how to search the mailing list in the new website? I didn't find the 
button.
   Because I failed to search the mailing list, I post the following question 
that may be discussed before. I used the pull code for simulation, here is my 
pull.ppa file:

verbose= no 
skip steps = 10
runtype= afm
group_1= G_pull
reference_group= Ref
reftype= com
pull_dim= Y Y Y

afm_rate1= 0.001 ;nm/ps
; Force constants in kJ/(mol*nm2)
afm_k1   = 4184
; Directions
afm_dir1 = 0.324761469  1.699368642 -1.350340856
afm_init1= -0.461723435 0.925478896 -0.835222495

My simulation time is 2 ns with a time step 2fs. If the unit of pull 
rate is nm/ps, the dummy atom should move 2 nm. However, I found that the dummy 
atom moved 4 nm! So, the unit of pull rate is (dt*nm)/(1fs*ps)? Right? I used 
Gromacs-3.3.1 for the simulation. Thanks!



Best regards,
2009-8-8


= 
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China 

Tel:   +86-10-62773574(O) 
Email: lidc02 at mails.tsinghua.edu.cn
=

  

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[gmx-users] Asymmetric potential for 512 dppc bilayer using martini

[Adwait Mevada]

Dear gmx-users,
I downloaded gro file containing 128 dppc lipids and 2000 waters from,  
Marrink's website, extracted the lipids and replicated using genconf,  
after minimization I added 2700 waters to it, minimized the system.  
Then gave an mdrun for 27ns. I did an potential analysis which results  
in an asymmetric bilayer profile. Can you tell me as to why am i  
getting such a result? I am

using Martini force field 2.0 and gromacs version 3.3.3.
I am attaching my mdp files and the potential  results.
# em.mdp ##
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;

; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator   = steep
; start time and timestep in ps
tinit= 0.0
dt   = 0.030
nsteps   = 10
; number of steps for center of mass motion removal =
nstcomm  = 1
comm-grps=

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstvout  = 2500
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1000
nstenergy= 1000
; Output frequency and precision for xtc file =
nstxtcout= 1000
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =

; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.

; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.3

; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.

; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.

; Temperature coupling   =
tcoupl   = no
; Groups to couple separately =
tc-grps  = DPPC
; Time constant (ps) and reference temperature (K) =
tau_t= 0.3
ref_t= 323
; Pressure coupling  =
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 3.0
compressibility  = 3e-5
ref_p= 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = no
gen_temp = 323
gen_seed = 666

; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.

constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30

#   md.mdp  #
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;

; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator   = md
; start time and timestep in ps
tinit= 0.0
dt   = 0.030
nsteps   = 90
; number of steps for center of mass motion removal =
nst

RE: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Berk Hess]

No, it should be exactly opposite.
I guess you must have done something wrong (forgot to run grompp or mdrun?).

Exclusions only affect non-bonded interactions.
Pair interactions do not influence and are not influenced by the exclusions 
section
or non-bonded interactions.

Berk

Date: Mon, 10 Aug 2009 20:38:57 +0800
Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs
of energy groups
From: nomad...@gmail.com
To: gmx-users@gromacs.org




2009/8/10 Mark Abraham 




Lee Soin wrote:

Hello!
Sorry to bother you again, but I have another question. I have written a
topology file of two water molecules to test the pair interaction. Here is

part of my topology file:

[ moleculetype ]
SOL  2
[ atoms ]
 1  opls_116  1  SOL  OW  1  -0.82
 2  opls_117  1  SOL  HW1  1  0.41
 3  opls_117  1  SOL  HW2  1  0.41
 4  opls_116  2  SOL  OW  2  -0.82

 5  opls_117  2  SOL  HW1  2  0.41
 6  opls_117  2  SOL  HW2  2  0.41
[ settles ]
 1  1  0.1  0.16330
 4  1  0.1  0.16330
[ exclusions ]
 1  2  3
 2  1  3
 3  1  2
 4  5  6
 5  4  6
 6  4  5

[ exclusions ]
1 4
[ pairs ]
 1  4  1

I have also changed the fudgeLJ and fudgeQQ to 1.0.
Originally, there is no pair interaction in this system. First I did a
simulation when the last 4 lines were removed, that is, I treated all the

interactions as non-bonded interactions. 

Since there is no bonded interaction between 1 and 4, your second [ exclusions 
] directive will not have any effect. Read section 5.4. Exclusions are 
cancellations only of interactions between bonded atoms. 



Then I added the last 4 lines
to specify the normal non-bonded interaction between atom 1 and 4 as pair

interaction in order to see whether that will affect the result. It turns
out that the results for the two cases are different. So did I miss
something, or are pair interactions and non-bonded interactions treated

differently by GROMACS?

mdrun is only reproducible if you tell it that you want it to be with "mdrun 
-reprod". So it is possible that your observation of different results is not 
(yet) meaningful.

 
Actually, I added the option "-reprod" and the results are reproducible. The 
results for the 
above-mentioned two cases are always different. So I am very confused.
 


However, I believe you've merely added a second identical non-bonded 
interaction between 1 and 4, so you will get different results regardless.

 
 
Then I tried to remove the two lines:
[ exclusions ]
1 4
And retained the pair interaction that I have defined. But this lead to no 
difference in the 
simulation result. Is it that the "exclusion" of non-bonded interaction between 
atom 1 and 
atom 4 didn't work?
On the other hand, in another set of simulations, I removed the pair 
interaction part:
[ pairs ]
 1  4  1
In this case, the presence and absence of the "exclusion" part do make a 
dramatic 

difference.
So can this conclusion be drawn: the presence of a pair interaction 
automatically eliminates 
the corresponding non-bonded interaction?
 
 


Mark
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Department of Physics
Nanjing University, China

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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Lee Soin]

2009/8/10 Mark Abraham 

>  Lee Soin wrote:
>
>> Hello!
>> Sorry to bother you again, but I have another question. I have written a
>> topology file of two water molecules to test the pair interaction. Here is
>> part of my topology file:
>>
>> [ moleculetype ]
>> SOL  2
>> [ atoms ]
>>  1  opls_116  1  SOL  OW  1  -0.82
>>  2  opls_117  1  SOL  HW1  1  0.41
>>  3  opls_117  1  SOL  HW2  1  0.41
>>  4  opls_116  2  SOL  OW  2  -0.82
>>  5  opls_117  2  SOL  HW1  2  0.41
>>  6  opls_117  2  SOL  HW2  2  0.41
>> [ settles ]
>>  1  1  0.1  0.16330
>>  4  1  0.1  0.16330
>> [ exclusions ]
>>  1  2  3
>>  2  1  3
>>  3  1  2
>>  4  5  6
>>  5  4  6
>>  6  4  5
>> [ exclusions ]
>> 1 4
>> [ pairs ]
>>  1  4  1
>>
>> I have also changed the fudgeLJ and fudgeQQ to 1.0.
>> Originally, there is no pair interaction in this system. First I did a
>> simulation when the last 4 lines were removed, that is, I treated all the
>> interactions as non-bonded interactions.
>>
>
> Since there is no bonded interaction between 1 and 4, your second [
> exclusions ] directive will not have any effect. Read section 5.4.
> Exclusions are cancellations only of interactions between bonded atoms.
>
> Then I added the last 4 lines
>> to specify the normal non-bonded interaction between atom 1 and 4 as pair
>> interaction in order to see whether that will affect the result. It turns
>> out that the results for the two cases are different. So did I miss
>> something, or are pair interactions and non-bonded interactions treated
>> differently by GROMACS?
>>
>
> mdrun is only reproducible if you tell it that you want it to be with
> "mdrun -reprod". So it is possible that your observation of different
> results is not (yet) meaningful.


Actually, I added the option "-reprod" and the results are reproducible. The
results for the
above-mentioned two cases are always different. So I am very confused.


>
>
> However, I believe you've merely added a second identical non-bonded
> interaction between 1 and 4, so you will get different results regardless.



Then I tried to remove the two lines:
[ exclusions ]
1 4
And retained the pair interaction that I have defined. But this lead to no
difference in the
simulation result. Is it that the "exclusion" of non-bonded interaction
between atom 1 and
atom 4 didn't work?
On the other hand, in another set of simulations, I removed the pair
interaction part:
[ pairs ]
 1  4  1
In this case, the presence and absence of the "exclusion" part do make a
dramatic
difference.
So can this conclusion be drawn: the presence of a pair interaction
automatically eliminates
the corresponding non-bonded interaction?




Mark
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-- 
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Department of Physics
Nanjing University, China
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RE: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Berk Hess]

> Date: Mon, 10 Aug 2009 22:11:57 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs  
> of energy groups
> 
> Berk Hess wrote:
> > 
> > 
> >> Date: Mon, 10 Aug 2009 20:52:31 +1000
> >> From: mark.abra...@anu.edu.au
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for 
> >> pairs   of energy groups
> >>
> >> Lee Soin wrote:
> >>> Hello!
> >>> Sorry to bother you again, but I have another question. I have written a
> >>> topology file of two water molecules to test the pair interaction. Here is
> >>> part of my topology file:
> >>>
> >>> [ moleculetype ]
> >>> SOL  2
> >>> [ atoms ]
> >>>   1  opls_116  1  SOL  OW  1  -0.82
> >>>   2  opls_117  1  SOL  HW1  1  0.41
> >>>   3  opls_117  1  SOL  HW2  1  0.41
> >>>   4  opls_116  2  SOL  OW  2  -0.82
> >>>   5  opls_117  2  SOL  HW1  2  0.41
> >>>   6  opls_117  2  SOL  HW2  2  0.41
> >>> [ settles ]
> >>>   1  1  0.1  0.16330
> >>>   4  1  0.1  0.16330
> >>> [ exclusions ]
> >>>   1  2  3
> >>>   2  1  3
> >>>   3  1  2
> >>>   4  5  6
> >>>   5  4  6
> >>>   6  4  5
> >>> [ exclusions ]
> >>> 1 4
> >>> [ pairs ]
> >>>   1  4  1
> >>>
> >>> I have also changed the fudgeLJ and fudgeQQ to 1.0.
> >>> Originally, there is no pair interaction in this system. First I did a
> >>> simulation when the last 4 lines were removed, that is, I treated all the
> >>> interactions as non-bonded interactions. 
> >> Since there is no bonded interaction between 1 and 4, your second [ 
> >> exclusions ] directive will not have any effect. Read section 5.4. 
> >> Exclusions are cancellations only of interactions between bonded atoms.
> >>
> > 
> > That is incorrect.
> > The exclusion line makes Gromacs excluded non-bonded interactions
> > between atoms 1 and 4. The [ exclusions ] section, although itself
> > "bonded" in some ways, has no relation at all with any other bonded
> > interactions.
> 
> True, 5.4 does point out that there are (in a sense) two kinds of 
> exclusions, viz "The exclusions for bonded particles are generated by 
> grompp for neighboring atoms up to a certain number of bonds away, as 
> defined in the [ moleculetype ] section in the topology file (see 
> 5.7.1).". Then the second paragraph goes on to point out the purpose of 
> [ exclusions ]: "Extra exclusions within a molecule can be added 
> manually in a [ exclusions ] section."
> 
> Perhaps the wording of this description could be improved, since the 
> sense of "[ exclusions ]" is actually "[ extra_exclusions ]"? A sentence 
> clarifying this before the full explanation would make things clearer:
> 
> "Exclusions
> 
> Additional pairs of particles from which non-bonded interactions are to 
> be excluded may be indicated under this directive. Some exclusions for 
> bonded particles may be generated by grompp for neighbouring atoms...
> 
> Such extra exclusions within a molecule can be added manually in the [ 
> exclusions ] list. Each line..."
> 
> Mark
> 

The phrase "The exclusions for bonded particles" is indeed confusing.
I now replaced it by:
The exclusions for non-bonded interactions are generated by grompp...

I also added a few more words in this section to clarify things.

Berk

> >>> Then I added the last 4 lines
> >>> to specify the normal non-bonded interaction between atom 1 and 4 as pair
> >>> interaction in order to see whether that will affect the result. It turns
> >>> out that the results for the two cases are different. So did I miss
> >>> something, or are pair interactions and non-bonded interactions treated
> >>> differently by GROMACS?
> >> mdrun is only reproducible if you tell it that you want it to be with 
> >> "mdrun -reprod". So it is possible that your observation of different 
> >> results is not (yet) meaningful.
> >>
> >> However, I believe you've merely added a second identical non-bonded 
> >> interaction between 1 and 4, so you will get different results regardless.
> >>
> >> Mark
> >> ___
> >> 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 
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http:

Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Mark Abraham]

Berk Hess wrote:




Date: Mon, 10 Aug 2009 20:52:31 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs
of energy groups

Lee Soin wrote:

Hello!
Sorry to bother you again, but I have another question. I have written a
topology file of two water molecules to test the pair interaction. Here is
part of my topology file:

[ moleculetype ]
SOL  2
[ atoms ]
  1  opls_116  1  SOL  OW  1  -0.82
  2  opls_117  1  SOL  HW1  1  0.41
  3  opls_117  1  SOL  HW2  1  0.41
  4  opls_116  2  SOL  OW  2  -0.82
  5  opls_117  2  SOL  HW1  2  0.41
  6  opls_117  2  SOL  HW2  2  0.41
[ settles ]
  1  1  0.1  0.16330
  4  1  0.1  0.16330
[ exclusions ]
  1  2  3
  2  1  3
  3  1  2
  4  5  6
  5  4  6
  6  4  5
[ exclusions ]
1 4
[ pairs ]
  1  4  1

I have also changed the fudgeLJ and fudgeQQ to 1.0.
Originally, there is no pair interaction in this system. First I did a
simulation when the last 4 lines were removed, that is, I treated all the
interactions as non-bonded interactions. 
Since there is no bonded interaction between 1 and 4, your second [ 
exclusions ] directive will not have any effect. Read section 5.4. 
Exclusions are cancellations only of interactions between bonded atoms.




That is incorrect.
The exclusion line makes Gromacs excluded non-bonded interactions
between atoms 1 and 4. The [ exclusions ] section, although itself
"bonded" in some ways, has no relation at all with any other bonded
interactions.


True, 5.4 does point out that there are (in a sense) two kinds of 
exclusions, viz "The exclusions for bonded particles are generated by 
grompp for neighboring atoms up to a certain number of bonds away, as 
defined in the [ moleculetype ] section in the topology file (see 
5.7.1).". Then the second paragraph goes on to point out the purpose of 
[ exclusions ]: "Extra exclusions within a molecule can be added 
manually in a [ exclusions ] section."


Perhaps the wording of this description could be improved, since the 
sense of "[ exclusions ]" is actually "[ extra_exclusions ]"? A sentence 
clarifying this before the full explanation would make things clearer:


"Exclusions

Additional pairs of particles from which non-bonded interactions are to 
be excluded may be indicated under this directive. Some exclusions for 
bonded particles may be generated by grompp for neighbouring atoms...


Such extra exclusions within a molecule can be added manually in the [ 
exclusions ] list. Each line..."


Mark


Then I added the last 4 lines
to specify the normal non-bonded interaction between atom 1 and 4 as pair
interaction in order to see whether that will affect the result. It turns
out that the results for the two cases are different. So did I miss
something, or are pair interactions and non-bonded interactions treated
differently by GROMACS?
mdrun is only reproducible if you tell it that you want it to be with 
"mdrun -reprod". So it is possible that your observation of different 
results is not (yet) meaningful.


However, I believe you've merely added a second identical non-bonded 
interaction between 1 and 4, so you will get different results regardless.


Mark
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[gmx-users] Re: Current status of CMAP

[Pär Bjelkmar]

The status of charmm with cmap is that it is implemented and present  
if one does git pull. The force field files of the distribution is  
outdated and should not be used. Instead interested users should  
contact me for the latest ones (different from the ones available from  
"my" webpage, http://www.dbb.su.se/User:Bjelkmar/ffcharmm). We have  
tested the code and are pretty convinced that the major parts for  
proteins are correct (0-step energies are correct compared to charmm  
in charmm). However, we're still working with it and testing termini,  
virtual sites, implicit solvent, etc. Our aim is to release it with  
gromacs 4.1 (although I have broken such "promises" before on this  
mailing list...).


Mark A: Actually I'm following the list but your suspicion is a valid  
one regarding the number of posts I have made... :D


Regards,
Pär Bjelkmar

7 aug 2009 kl. 17.39 skrev gmx-users-requ...@gromacs.org:


Hi all,

I know this has been up on the list before, but I haven't been able to
get some definite answer - What's the current status of the
implementation of CHARMM-type CMAPs? I note that people (especially P.
Bjelkmar as it seems) have done a great job implementing the other
peculiarities of the CHARMM force fields, but it's still that final
piece missing. There are several references to CMAP in the source  
code,
but I guess it's not fully implemented yet. I just wonder if it will  
be

ready anytime soon?

I would be glad to help anyway I can, at least by doing some testing.

Best regards,
Jakob Wohlert


<><><><><><><><><><><><><><><><><><>
Pär Bjelkmar, PhD student   

Stockholm Center for Biomembrane Research,
Stockholm Bioinformatics Center,
Department of Biochemistry and Biophysics,
Stockholm University

Tel:+46-8-16 2746   
Fax: +46-8-15 3679  
E-mail: bjelk...@cbr.su.se  
Home: http://www.dbb.su.se/User:Bjelkmar
<><><><><><><><><><><><><><><><><><>

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RE: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Berk Hess]

> Date: Mon, 10 Aug 2009 20:52:31 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs  
> of energy groups
> 
> Lee Soin wrote:
> > Hello!
> > Sorry to bother you again, but I have another question. I have written a
> > topology file of two water molecules to test the pair interaction. Here is
> > part of my topology file:
> > 
> > [ moleculetype ]
> > SOL  2
> > [ atoms ]
> >   1  opls_116  1  SOL  OW  1  -0.82
> >   2  opls_117  1  SOL  HW1  1  0.41
> >   3  opls_117  1  SOL  HW2  1  0.41
> >   4  opls_116  2  SOL  OW  2  -0.82
> >   5  opls_117  2  SOL  HW1  2  0.41
> >   6  opls_117  2  SOL  HW2  2  0.41
> > [ settles ]
> >   1  1  0.1  0.16330
> >   4  1  0.1  0.16330
> > [ exclusions ]
> >   1  2  3
> >   2  1  3
> >   3  1  2
> >   4  5  6
> >   5  4  6
> >   6  4  5
> > [ exclusions ]
> > 1 4
> > [ pairs ]
> >   1  4  1
> > 
> > I have also changed the fudgeLJ and fudgeQQ to 1.0.
> > Originally, there is no pair interaction in this system. First I did a
> > simulation when the last 4 lines were removed, that is, I treated all the
> > interactions as non-bonded interactions. 
> 
> Since there is no bonded interaction between 1 and 4, your second [ 
> exclusions ] directive will not have any effect. Read section 5.4. 
> Exclusions are cancellations only of interactions between bonded atoms.
> 

That is incorrect.
The exclusion line makes Gromacs excluded non-bonded interactions
between atoms 1 and 4. The [ exclusions ] section, although itself
"bonded" in some ways, has no relation at all with any other bonded
interactions.

Berk

> > Then I added the last 4 lines
> > to specify the normal non-bonded interaction between atom 1 and 4 as pair
> > interaction in order to see whether that will affect the result. It turns
> > out that the results for the two cases are different. So did I miss
> > something, or are pair interactions and non-bonded interactions treated
> > differently by GROMACS?
> 
> mdrun is only reproducible if you tell it that you want it to be with 
> "mdrun -reprod". So it is possible that your observation of different 
> results is not (yet) meaningful.
> 
> However, I believe you've merely added a second identical non-bonded 
> interaction between 1 and 4, so you will get different results regardless.
> 
> Mark
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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Mark Abraham]

Lee Soin wrote:

Hello!
Sorry to bother you again, but I have another question. I have written a
topology file of two water molecules to test the pair interaction. Here is
part of my topology file:

[ moleculetype ]
SOL  2
[ atoms ]
  1  opls_116  1  SOL  OW  1  -0.82
  2  opls_117  1  SOL  HW1  1  0.41
  3  opls_117  1  SOL  HW2  1  0.41
  4  opls_116  2  SOL  OW  2  -0.82
  5  opls_117  2  SOL  HW1  2  0.41
  6  opls_117  2  SOL  HW2  2  0.41
[ settles ]
  1  1  0.1  0.16330
  4  1  0.1  0.16330
[ exclusions ]
  1  2  3
  2  1  3
  3  1  2
  4  5  6
  5  4  6
  6  4  5
[ exclusions ]
1 4
[ pairs ]
  1  4  1

I have also changed the fudgeLJ and fudgeQQ to 1.0.
Originally, there is no pair interaction in this system. First I did a
simulation when the last 4 lines were removed, that is, I treated all the
interactions as non-bonded interactions. 


Since there is no bonded interaction between 1 and 4, your second [ 
exclusions ] directive will not have any effect. Read section 5.4. 
Exclusions are cancellations only of interactions between bonded atoms.



Then I added the last 4 lines
to specify the normal non-bonded interaction between atom 1 and 4 as pair
interaction in order to see whether that will affect the result. It turns
out that the results for the two cases are different. So did I miss
something, or are pair interactions and non-bonded interactions treated
differently by GROMACS?


mdrun is only reproducible if you tell it that you want it to be with 
"mdrun -reprod". So it is possible that your observation of different 
results is not (yet) meaningful.


However, I believe you've merely added a second identical non-bonded 
interaction between 1 and 4, so you will get different results regardless.


Mark
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Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Lee Soin]

Hello!
Sorry to bother you again, but I have another question. I have written a
topology file of two water molecules to test the pair interaction. Here is
part of my topology file:

[ moleculetype ]
SOL  2
[ atoms ]
  1  opls_116  1  SOL  OW  1  -0.82
  2  opls_117  1  SOL  HW1  1  0.41
  3  opls_117  1  SOL  HW2  1  0.41
  4  opls_116  2  SOL  OW  2  -0.82
  5  opls_117  2  SOL  HW1  2  0.41
  6  opls_117  2  SOL  HW2  2  0.41
[ settles ]
  1  1  0.1  0.16330
  4  1  0.1  0.16330
[ exclusions ]
  1  2  3
  2  1  3
  3  1  2
  4  5  6
  5  4  6
  6  4  5
[ exclusions ]
1 4
[ pairs ]
  1  4  1

I have also changed the fudgeLJ and fudgeQQ to 1.0.
Originally, there is no pair interaction in this system. First I did a
simulation when the last 4 lines were removed, that is, I treated all the
interactions as non-bonded interactions. Then I added the last 4 lines
to specify the normal non-bonded interaction between atom 1 and 4 as pair
interaction in order to see whether that will affect the result. It turns
out that the results for the two cases are different. So did I miss
something, or are pair interactions and non-bonded interactions treated
differently by GROMACS?
Thanks in advance.

2009/7/28 Mark Abraham 

> Lee Soin wrote:
>
>> So there is no place to specify electrostatic interactions for pair
>> interactions?
>>
>
> No. The charges are specified in the [ atoms ] directive. Read the example
> in chapter 5.
>
>
> Mark
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-- 
SUN Li
Department of Physics
Nanjing University, China
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Re: [gmx-users] Strange MPI problems. . .

[Carsten Kutzner]

Hi,

probably there is just a problem with node126 on your system.  
mx_open_endpoint
errors can occur if there is still another (dead?) job occupying the  
myrinet interface.
You should check for such jobs on the node, kill them, and if it still  
does not work,

reboot that node.

Alternatively, if you just submit the same job again (and it ends up  
on different nodes),

I would guess that it runs fine.

Carsten


On Aug 10, 2009, at 4:58 AM, Marc Charendoff wrote:


Hello,


   I am trying to perform a position restrained MD run on our  
school cluster on a system I have successfully run on before. The  
only difference is that this new run uses the 43a1 force field (the  
original used gmx). All my preprocessing has gone well, but when I  
submit to the cluster, my log file shows the following:


[node126:13068] Error in mx_open_endpoint (error Failure querying MX  
driver(wrong driver?))
[node126:13068] mca_btl_mx_init: mx_open_endpoint() failed with  
status=1

warning:regcache incompatible with malloc
NNODES=2, MYRANK=0, HOSTNAME=node126
NNODES=2, MYRANK=1, HOSTNAME=node056
NODEID=0 argc=12
NODEID=1 argc=12
[node126][0,1,0][btl_tcp_endpoint.c: 
572:mca_btl_tcp_endpoint_complete_connect] connect() failed with  
errno=113


I immediately reran the old calculation (gmx) which worked just  
fine. I should also note the my energy minimization run (43a1) on a  
single processor ran ok. Any guidance anyone could provide would be  
appreciated.


Much Thanks,

Marc
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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