Re: [gmx-users] RMSD with Vsite vs No Vsites

[Sikandar Mashayak]

well the deviations are about more than 0.5 nm..

On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai  wrote:

> On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
> > Hi
> >
> > As a test case, I did two simulations one the usual Protein in Water and
> other with Vsites at COM of each monomer but these Vsites dont interact with
> anyone else. I was expecting results of these two should match almost
> exactly, but when I compare the rmsd for Protein there seems to be
> discrepancy.
> >
> > I once again checked my Vsites definitions and set up, there doesnt seem
> to be any error in definition as per my understanding.
> >
> > Is there any other reason that may be causing the mismatch? Or I may have
> done something wrong in the setting up Vsites simulations.
> >
> > thanks
> > sikandar
>
> how large are the RMSD deviations? are they statistically significant for
> your needs? (i.e. if you only are about 1A scales, then RMSD differences
> < 0.05nm would be meaningless...
>
> --
> ===
> Peter C. Lai | University of Alabama-Birmingham
> Programmer/Analyst   | BEC 257
> Genetics, Div. of Research   | 1150 10th Avenue South
> p...@uab.edu  | Birmingham AL 35294-4461
> (205) 690-0808   |
> ===
>
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] DO_DSSP

[battis...@libero.it]

Dear all,

I'm trying install do_dssp on my pc.I followed the steps indicated in the page:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html
>> 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf dsspcmbi.tar.gz
>> 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./DsspCompileGCC
>> 3.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# cp dsspcmbi dssp
>> 4.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# mv dssp /usr/local/bin
and the program work well.
Now my question:How the program use the file that I downloaded from the 
web-page:http://swift.cmbi.ru.nl/gv/dssp/   using the indicated instruction? (I 
found this page from 
http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP)

rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/

The link  rsync://rsync.cmbi.ru.nl/dssp/  is one of the best  database to 
calculate the angle into the secondary structures and so to define that, isn't 
it?

Thanks,
Anna
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] NMA problem

[Rashmi]

Dear All,

I am using MM/PBSA to calculate protein-ligand binding affinnity using
GROMACS. I got stuck at entropy calculation stage, which can be broadly done
by two mthods i.e. Normal Mode Analysis and Quasi-Harmonic method.

Can anyone let me know that how minimization using distance based dielectric
(r-dielectric) with a prefactor of  4 can be done for normal modes
calculation using GROMACS.

Thanks in advance for any valuable suggeations.

-- 
With Regards,

Rashmi Kumari
Research Scholar
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi- 110067.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] RMSD with Vsite vs No Vsites

[Mark Abraham]

On 6/05/2011 5:32 PM, Sikandar Mashayak wrote:

well the deviations are about more than 0.5 nm..


And what does gmxcheck -s1 -s2 show?

Mark



On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai > wrote:


On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
> Hi
>
> As a test case, I did two simulations one the usual Protein in
Water and other with Vsites at COM of each monomer but these
Vsites dont interact with anyone else. I was expecting results of
these two should match almost exactly, but when I compare the rmsd
for Protein there seems to be discrepancy.
>
> I once again checked my Vsites definitions and set up, there
doesnt seem to be any error in definition as per my understanding.
>
> Is there any other reason that may be causing the mismatch? Or I
may have done something wrong in the setting up Vsites simulations.
>
> thanks
> sikandar

how large are the RMSD deviations? are they statistically
significant for
your needs? (i.e. if you only are about 1A scales, then RMSD
differences
< 0.05nm would be meaningless...

--
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu   | Birmingham AL
35294-4461
(205) 690-0808|
===




-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] DO_DSSP

[Mark Abraham]

On 6/05/2011 5:22 PM, battis...@libero.it wrote:


Dear all,


I'm trying install do_dssp on my pc.

I followed the steps indicated in the page:

http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html


>> 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf 
dsspcmbi.tar.gz

>> 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./DsspCompileGCC
>> 3.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# cp dsspcmbi dssp
>> 4.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# mv dssp 
/usr/local/bin



and the program work well.


Now my question:

How the program use the file that I downloaded from the web-page:

http://swift.cmbi.ru.nl/gv/dssp/   using the indicated instruction?



GROMACS doesn't. Read the DSSP documentation about what it is providing.

(I found this page from 
http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP)


rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/

The link  rsync://rsync.cmbi.ru.nl/dssp/  is one of the best 
//database //to calculate the angle into the secondary structures and 
so to define that, isn't it?




One doesn't need a database to calculate angles.

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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Nitrate ion

[Maria Hamilton]

Hi all

I need  .PDB and .itp file of Nitrate ions. Do any one have them?

Thanks alot

Best,

Maria
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] DO_DSSP

[anna]

Thank you very much!

Anna


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites

[Gavin Melaugh]

Hi Sikandar

A couple of questions regarding the virtual sites.
1) Do I have to number the virtual site in accordance with the atom
indices of the rest of the molecule?
2) Is the parameters for the virtual site declared in the atomtypes
directive?

Cheers

Gavin

Sikandar Mashayak wrote:
>  in doing so .. by default all pair interactions with virtual sites
> would result in zero forces except those between atoms defined in
> [nonbond_params]
>
> On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak
> mailto:symasha...@gmail.com>> wrote:
>
> hey
>
> another approach to do this without using energy group exclusion
> is to define non-bonded interactions parameter explicitly between
> atoms in ffnonbonded.itp file. You can specify sigma and epsilon
> to be zero in virtual sites atoms definition and specify
> individual pair interactions parameters using non-bonded
> interactions like following ...
>
> ; virtual site
> VS1 00  0   D   0   0
> VS2  00  0   D   0   0
> VS3 00  0   D   0   0
>
> [ nonbond_params ]
> VS1 C 1   1.0 0.25
> VS2 C 1   1.0 0.25
> VS2 C 1   1.0 0.25
>
> --
> sikandar
>
> On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh
> mailto:gmelaug...@qub.ac.uk>> wrote:
>
> Hi Justin
>
> I do not intend to have charges on the sites. All I want is;
> when a CH3 group gets close to the site it feels a repulsive
> force. I
> have calculated a sigma and epsilon value for this interaction.
>
> Gavin
>
> Justin A. Lemkul wrote:
> >
> >
> > Gavin Melaugh wrote:
> >> Hi Justin
> >>
> >> I am reading the manual at the moment. I want to include
> some virtual
> >> sites in my molecule so that only surrounding CH3s atom
> type C3 interact
> >> with then. All other atoms I don't want to interact with
> them. Do I
> >> create energy groups in the index file called say "virtual
> sites" and
> >> "exclusions", and list all the indices of the atom types
> that I don't
> >> want to interact with the virtual site in one group and all
> the virtual
> >> sites in another.
> >> e.g
> >>
> >> [virtual sites]
> >> 17 18 19 20
> >>
> >> [virtsite_exclus]
> >> 1 2 3 4 5 6 7 8 9 .
> >>
> >
> > In a general sense, yes, that's the right approach.  Note
> that if any
> > of these sites is charged and/or you're using PME, then this
> whole
> > exclusion thing goes out the window, as has been discussed
> several
> > times in recent days.  Using energygrp_excl applies only to
> > short-range nonbonded interactions.  If you need complete
> exclusion,
> > you may have to look into tabulated potentials if this is
> the case.
> >
> > -Justin
> >
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> 
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
> .
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Hi

I am trying to alter a topology to include 3 virtual sites and I have a
few queries, the answers to which are not obvious form the manual.
Do I declare the virtual sites in the atomtypes directive like so

;type mass   charge  ptype sigma(nm)
epsilon(kjmol-1)
   CB 12.011000  0.00   A  0.355000  0.292880
   CA 12.011000 -0.115000   A  0.355000  0.292880
   VS1 0.00.0V 
0.0   0.0
   VS2 0.00.0V 
0.0   0.0
   VS3 0.00.0V 
0.0   0.0

Do I give them an index number in the atoms directive e.g.

[atoms]
; atomnr  type   resnr  residue   namecgnr charge mass
1  CA   1   CGECA   1 -0.1150 12.0110
2  CB   1   CGECB   1  0. 12.0110
3  CA   1   CGECA   2 -0.1150 12.0110
4  CB   1   CGECB   2  0. 12.0110
5  CA   1   CGECA   3 -0.1150 12.0110
 ..
 ..
  229  VS1  2   VIRVS1 85  0.  0.
  230  VS2  3   VIRVS2 86  0.  0.
  231  VS3  4   VIRVS3 87  0.  0.

Then if I want to set up a virtual site between the COG of 3 atoms do I
do it in the following way

[virtual_sitesn]
;site COG of three hydrogens at window
;site  i jkfunc
229740   581
230   1025   551
231   2837   521


Cheers

Gavin



Gavin Melaugh wrote:
> Hi Sikandar
>
> A couple of questions regarding the virtual sites.
> 1) Do I have to number the virtual site in accordance with the atom
> indices of the rest of the molecule?
> 2) Is the parameters for the virtual site declared in the atomtypes
> directive?
>
> Cheers
>
> Gavin
>
> Sikandar Mashayak wrote:
>   
>>  in doing so .. by default all pair interactions with virtual sites
>> would result in zero forces except those between atoms defined in
>> [nonbond_params]
>>
>> On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak
>> mailto:symasha...@gmail.com>> wrote:
>>
>> hey
>>
>> another approach to do this without using energy group exclusion
>> is to define non-bonded interactions parameter explicitly between
>> atoms in ffnonbonded.itp file. You can specify sigma and epsilon
>> to be zero in virtual sites atoms definition and specify
>> individual pair interactions parameters using non-bonded
>> interactions like following ...
>>
>> ; virtual site
>> VS1 00  0   D   0   0
>> VS2  00  0   D   0   0
>> VS3 00  0   D   0   0
>>
>> [ nonbond_params ]
>> VS1 C 1   1.0 0.25
>> VS2 C 1   1.0 0.25
>> VS2 C 1   1.0 0.25
>>
>> --
>> sikandar
>>
>> On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh
>> mailto:gmelaug...@qub.ac.uk>> wrote:
>>
>> Hi Justin
>>
>> I do not intend to have charges on the sites. All I want is;
>> when a CH3 group gets close to the site it feels a repulsive
>> force. I
>> have calculated a sigma and epsilon value for this interaction.
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>> >
>> >
>> > Gavin Melaugh wrote:
>> >> Hi Justin
>> >>
>> >> I am reading the manual at the moment. I want to include
>> some virtual
>> >> sites in my molecule so that only surrounding CH3s atom
>> type C3 interact
>> >> with then. All other atoms I don't want to interact with
>> them. Do I
>> >> create energy groups in the index file called say "virtual
>> sites" and
>> >> "exclusions", and list all the indices of the atom types
>> that I don't
>> >> want to interact with the virtual site in one group and all
>> the virtual
>> >> sites in another.
>> >> e.g
>> >>
>> >> [virtual sites]
>> >> 17 18 19 20
>> >>
>> >> [virtsite_exclus]
>> >> 1 2 3 4 5 6 7 8 9 .
>> >>
>> >
>> > In a general sense, yes, that's the right approach.  Note
>> that if any
>> > of these sites is charged and/or you're using PME, then this
>> whole
>> > exclusion thing goes out the window, as has been discussed
>> several
>> > times in recent days.  Using energygrp_excl applies only to
>> > short-range nonbonded interactions.  If you need complete
>> exclusion,
>> > you may have to look into tabulated potentials if this is
>> the case.
>> >
>>  

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Hi
Having tried to run grompp using the data below I keep getting the
following error
Fatal error:
Unknown vsiten type 7
Does anyone know why this might be?

Gavin

Gavin Melaugh wrote:
> Hi
>
> I am trying to alter a topology to include 3 virtual sites and I have a
> few queries, the answers to which are not obvious form the manual.
> Do I declare the virtual sites in the atomtypes directive like so
>
> ;type mass   charge  ptype sigma(nm)
> epsilon(kjmol-1)
>CB 12.011000  0.00   A  0.355000  0.292880
>CA 12.011000 -0.115000   A  0.355000  0.292880
>VS1 0.00.0V 
> 0.0   0.0
>VS2 0.00.0V 
> 0.0   0.0
>VS3 0.00.0V 
> 0.0   0.0
>
> Do I give them an index number in the atoms directive e.g.
>
> [atoms]
> ; atomnr  type   resnr  residue   namecgnr charge mass
> 1  CA   1   CGECA   1 -0.1150 12.0110
> 2  CB   1   CGECB   1  0. 12.0110
> 3  CA   1   CGECA   2 -0.1150 12.0110
> 4  CB   1   CGECB   2  0. 12.0110
> 5  CA   1   CGECA   3 -0.1150 12.0110
>  ..
>  ..
>   229  VS1  2   VIRVS1 85  0.  0.
>   230  VS2  3   VIRVS2 86  0.  0.
>   231  VS3  4   VIRVS3 87  0.  0.
>
> Then if I want to set up a virtual site between the COG of 3 atoms do I
> do it in the following way
>
> [virtual_sitesn]
> ;site COG of three hydrogens at window
> ;site  i jkfunc
> 229740   581
> 230   1025   551
> 231   2837   521
>
>
> Cheers
>
> Gavin
>
>
>
> Gavin Melaugh wrote:
>   
>> Hi Sikandar
>>
>> A couple of questions regarding the virtual sites.
>> 1) Do I have to number the virtual site in accordance with the atom
>> indices of the rest of the molecule?
>> 2) Is the parameters for the virtual site declared in the atomtypes
>> directive?
>>
>> Cheers
>>
>> Gavin
>>
>> Sikandar Mashayak wrote:
>>   
>> 
>>>  in doing so .. by default all pair interactions with virtual sites
>>> would result in zero forces except those between atoms defined in
>>> [nonbond_params]
>>>
>>> On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak
>>> mailto:symasha...@gmail.com>> wrote:
>>>
>>> hey
>>>
>>> another approach to do this without using energy group exclusion
>>> is to define non-bonded interactions parameter explicitly between
>>> atoms in ffnonbonded.itp file. You can specify sigma and epsilon
>>> to be zero in virtual sites atoms definition and specify
>>> individual pair interactions parameters using non-bonded
>>> interactions like following ...
>>>
>>> ; virtual site
>>> VS1 00  0   D   0   0
>>> VS2  00  0   D   0   0
>>> VS3 00  0   D   0   0
>>>
>>> [ nonbond_params ]
>>> VS1 C 1   1.0 0.25
>>> VS2 C 1   1.0 0.25
>>> VS2 C 1   1.0 0.25
>>>
>>> --
>>> sikandar
>>>
>>> On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh
>>> mailto:gmelaug...@qub.ac.uk>> wrote:
>>>
>>> Hi Justin
>>>
>>> I do not intend to have charges on the sites. All I want is;
>>> when a CH3 group gets close to the site it feels a repulsive
>>> force. I
>>> have calculated a sigma and epsilon value for this interaction.
>>>
>>> Gavin
>>>
>>> Justin A. Lemkul wrote:
>>> >
>>> >
>>> > Gavin Melaugh wrote:
>>> >> Hi Justin
>>> >>
>>> >> I am reading the manual at the moment. I want to include
>>> some virtual
>>> >> sites in my molecule so that only surrounding CH3s atom
>>> type C3 interact
>>> >> with then. All other atoms I don't want to interact with
>>> them. Do I
>>> >> create energy groups in the index file called say "virtual
>>> sites" and
>>> >> "exclusions", and list all the indices of the atom types
>>> that I don't
>>> >> want to interact with the virtual site in one group and all
>>> the virtual
>>> >> sites in another.
>>> >> e.g
>>> >>
>>> >> [virtual sites]
>>> >> 17 18 19 20
>>> >>
>>> >> [virtsite_exclus]
>>> >> 1 2 3 4 5 6 7 8 9 .
>>> >>
>>> >
>>> > In a general sense, yes, that's the right approach.  Note
>>> that if any
>>> > of these sites is charged and/or you're using PME, then this
>>> wh

Re: [gmx-users] virtual sites set up for topology file

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi
Having tried to run grompp using the data below I keep getting the
following error
Fatal error:
Unknown vsiten type 7
Does anyone know why this might be?



Your [virtual_sites] directive is not correct, either in its name (no such thing 
as "virtual_sitesn" - the "n" should be replaced by a digit indicating the type) 
or in the contents.  See manual section 5.2.2.


-Justin


Gavin

Gavin Melaugh wrote:

Hi

I am trying to alter a topology to include 3 virtual sites and I have a
few queries, the answers to which are not obvious form the manual.
Do I declare the virtual sites in the atomtypes directive like so

;type mass   charge  ptype sigma(nm)
epsilon(kjmol-1)

   CB 12.011000  0.00   A  0.355000  0.292880
   CA 12.011000 -0.115000   A  0.355000  0.292880
   VS1 0.00.0V 
0.0   0.0
   VS2 0.00.0V 
0.0   0.0
   VS3 0.00.0V 
0.0   0.0


Do I give them an index number in the atoms directive e.g.

[atoms]
; atomnr  type   resnr  residue   namecgnr charge mass
1  CA   1   CGECA   1 -0.1150 12.0110
2  CB   1   CGECB   1  0. 12.0110
3  CA   1   CGECA   2 -0.1150 12.0110
4  CB   1   CGECB   2  0. 12.0110
5  CA   1   CGECA   3 -0.1150 12.0110
 ..
 ..
  229  VS1  2   VIRVS1 85  0.  0.
  230  VS2  3   VIRVS2 86  0.  0.
  231  VS3  4   VIRVS3 87  0.  0.

Then if I want to set up a virtual site between the COG of 3 atoms do I
do it in the following way

[virtual_sitesn]
;site COG of three hydrogens at window
;site  i jkfunc
229740   581
230   1025   551
231   2837   521


Cheers

Gavin



Gavin Melaugh wrote:
  

Hi Sikandar

A couple of questions regarding the virtual sites.
1) Do I have to number the virtual site in accordance with the atom
indices of the rest of the molecule?
2) Is the parameters for the virtual site declared in the atomtypes
directive?

Cheers

Gavin

Sikandar Mashayak wrote:
  


 in doing so .. by default all pair interactions with virtual sites
would result in zero forces except those between atoms defined in
[nonbond_params]

On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak
mailto:symasha...@gmail.com>> wrote:

hey

another approach to do this without using energy group exclusion
is to define non-bonded interactions parameter explicitly between
atoms in ffnonbonded.itp file. You can specify sigma and epsilon
to be zero in virtual sites atoms definition and specify
individual pair interactions parameters using non-bonded
interactions like following ...

; virtual site
VS1 00  0   D   0   0
VS2  00  0   D   0   0
VS3 00  0   D   0   0

[ nonbond_params ]
VS1 C 1   1.0 0.25
VS2 C 1   1.0 0.25
VS2 C 1   1.0 0.25

--
sikandar

On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh
mailto:gmelaug...@qub.ac.uk>> wrote:

Hi Justin

I do not intend to have charges on the sites. All I want is;
when a CH3 group gets close to the site it feels a repulsive
force. I
have calculated a sigma and epsilon value for this interaction.

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> I am reading the manual at the moment. I want to include
some virtual
>> sites in my molecule so that only surrounding CH3s atom
type C3 interact
>> with then. All other atoms I don't want to interact with
them. Do I
>> create energy groups in the index file called say "virtual
sites" and
>> "exclusions", and list all the indices of the atom types
that I don't
>> want to interact with the virtual site in one group and all
the virtual
>> sites in another.
>> e.g
>>
>> [virtual sites]
>> 17 18 19 20
>>
>> [virtsite_exclus]
>> 1 2 3 4 5 6 7 8 9 .
>>
>
> In a general sense, yes, that's the right approach.  Note
that if any
> of these sites is charged and/or you're using PME, then this
whole
> exclusion thing goes out the window, as has been discussed
several
> times in recent days.  Using energygrp_excl applies only t

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Hi Justin

Thanks for the reply. To create a virtual site at the centre of geometry
of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
the index of the site, the index of the three atoms and then the
function type 1 which determines that it is COG.
Or as I now realise. State [virtual_site3], site index atom indices, and
function 1. The fact that there are no parameters then by default must
mean it is COG. Is this correct?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi
>> Having tried to run grompp using the data below I keep getting the
>> following error
>> Fatal error:
>> Unknown vsiten type 7
>> Does anyone know why this might be?
>>
>
> Your [virtual_sites] directive is not correct, either in its name (no
> such thing as "virtual_sitesn" - the "n" should be replaced by a digit
> indicating the type) or in the contents.  See manual section 5.2.2.
>
> -Justin
>
>> Gavin
>>
>> Gavin Melaugh wrote:
>>> Hi
>>>
>>> I am trying to alter a topology to include 3 virtual sites and I have a
>>> few queries, the answers to which are not obvious form the manual.
>>> Do I declare the virtual sites in the atomtypes directive like so
>>>
>>> ;type mass   charge  ptype sigma(nm)   
>>> epsilon(kjmol-1)
>>>CB 12.011000  0.00   A  0.355000  0.292880
>>>CA 12.011000 -0.115000   A  0.355000  0.292880
>>>VS1 0.00.0V
>>> 0.0   0.0
>>>VS2 0.00.0V
>>> 0.0   0.0
>>>VS3 0.00.0V
>>> 0.0   0.0
>>>
>>> Do I give them an index number in the atoms directive e.g.
>>>
>>> [atoms]
>>> ; atomnr  type   resnr  residue   namecgnr charge mass
>>> 1  CA   1   CGECA   1 -0.1150 12.0110
>>> 2  CB   1   CGECB   1  0. 12.0110
>>> 3  CA   1   CGECA   2 -0.1150 12.0110
>>> 4  CB   1   CGECB   2  0. 12.0110
>>> 5  CA   1   CGECA   3 -0.1150 12.0110
>>>  ..
>>>  ..
>>>   229  VS1  2   VIRVS1 85  0.  0.
>>>   230  VS2  3   VIRVS2 86  0.  0.
>>>   231  VS3  4   VIRVS3 87  0.  0.
>>>
>>> Then if I want to set up a virtual site between the COG of 3 atoms do I
>>> do it in the following way
>>>
>>> [virtual_sitesn]
>>> ;site COG of three hydrogens at window
>>> ;site  i jkfunc
>>> 229740   581
>>> 230   1025   551
>>> 231   2837   521
>>>
>>>
>>> Cheers
>>>
>>> Gavin
>>>
>>>
>>>
>>> Gavin Melaugh wrote:
>>>  
 Hi Sikandar

 A couple of questions regarding the virtual sites.
 1) Do I have to number the virtual site in accordance with the atom
 indices of the rest of the molecule?
 2) Is the parameters for the virtual site declared in the atomtypes
 directive?

 Cheers

 Gavin

 Sikandar Mashayak wrote:
  
>  in doing so .. by default all pair interactions with virtual sites
> would result in zero forces except those between atoms defined in
> [nonbond_params]
>
> On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak
> mailto:symasha...@gmail.com>> wrote:
>
> hey
>
> another approach to do this without using energy group exclusion
> is to define non-bonded interactions parameter explicitly between
> atoms in ffnonbonded.itp file. You can specify sigma and epsilon
> to be zero in virtual sites atoms definition and specify
> individual pair interactions parameters using non-bonded
> interactions like following ...
>
> ; virtual site
> VS1 00  0   D   0   0
> VS2  00  0   D  
> 0   0
> VS3 00  0   D   0   0
>
> [ nonbond_params ]
> VS1 C 1   1.0 0.25
> VS2 C 1   1.0 0.25
> VS2 C 1   1.0 0.25
>
> --
> sikandar
>
> On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh
> mailto:gmelaug...@qub.ac.uk>> wrote:
>
> Hi Justin
>
> I do not intend to have charges on the sites. All I want is;
> when a CH3 group gets close to the site it feels a repulsive
> force. I
> have calculated a sigma and epsilon value for this
> interaction.
>
> Gavin
>
> Justin A. Lemkul wrote:
> >
> >
> > Gavin Melaugh wrote:
> >> Hi Justin
> >>
> >> I am

Re: [gmx-users] virtual sites set up for topology file

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Justin

Thanks for the reply. To create a virtual site at the centre of geometry
of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
the index of the site, the index of the three atoms and then the
function type 1 which determines that it is COG.


OK, so that would seem to be right from Table 5.6, but it's not discussed 
anywhere else, so I suspect that it may be a feature that either got broken 
along the way, or for some other reason doesn't work, since it's not :)



Or as I now realise. State [virtual_site3], site index atom indices, and
function 1. The fact that there are no parameters then by default must
mean it is COG. Is this correct?



I don't know if [virtual_sites3] can be specified without any parameters.  It 
seems to me that this shouldn't be correct.  It never hurts to try.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Justin

I have tried this but I am now getting different errors. I take it that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?
I index the virtual sites in the atoms directive in accordance with the
rest of the molecule. atom numbers go from 1-228, therefore I label the
3 virtual sites 229 to231.
The error I get now is

Atom index (229) in virtual_sites3 out of bounds (1-228).
This probably means that you have inserted topology section "virtual_sites3"
in a part belonging to a different molecule than you intended to.
In that case move the "virtual_sites3" section to the right molecule.

Do I have to have the virtual sites in the gro file also? This doesn't
make sense

Gavin
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Thanks for the reply. To create a virtual site at the centre of geometry
>> of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
>> the index of the site, the index of the three atoms and then the
>> function type 1 which determines that it is COG.
>
> OK, so that would seem to be right from Table 5.6, but it's not
> discussed anywhere else, so I suspect that it may be a feature that
> either got broken along the way, or for some other reason doesn't
> work, since it's not :)
>
>> Or as I now realise. State [virtual_site3], site index atom indices, and
>> function 1. The fact that there are no parameters then by default must
>> mean it is COG. Is this correct?
>>
>
> I don't know if [virtual_sites3] can be specified without any
> parameters.  It seems to me that this shouldn't be correct.  It never
> hurts to try.
>
> -Justin
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Justin A. Lemkul]

Gavin Melaugh wrote:

Justin

I have tried this but I am now getting different errors. I take it that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?


Virtual sites are included in all the force fields already, but if you want some 
custom name, then yes, include them in a new [atomtypes] directive.  I see no 
reason to create three distinct, but identical, types as you have.



I index the virtual sites in the atoms directive in accordance with the
rest of the molecule. atom numbers go from 1-228, therefore I label the
3 virtual sites 229 to231.
The error I get now is

Atom index (229) in virtual_sites3 out of bounds (1-228).
This probably means that you have inserted topology section "virtual_sites3"
in a part belonging to a different molecule than you intended to.
In that case move the "virtual_sites3" section to the right molecule.

Do I have to have the virtual sites in the gro file also? This doesn't
make sense



Yes, you need their coordinates as part of the initial state.

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site  when I stated that it was to be at the
COG  of the  3 atoms in  the [virtual_sitesn] directive.

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> I have tried this but I am now getting different errors. I take it that:
>> I specify the virtual sites in the atomtypes directive as I have seen
>> from examples?
>
> Virtual sites are included in all the force fields already, but if you
> want some custom name, then yes, include them in a new [atomtypes]
> directive.  I see no reason to create three distinct, but identical,
> types as you have.
>
>> I index the virtual sites in the atoms directive in accordance with the
>> rest of the molecule. atom numbers go from 1-228, therefore I label the
>> 3 virtual sites 229 to231.
>> The error I get now is
>>
>> Atom index (229) in virtual_sites3 out of bounds (1-228).
>> This probably means that you have inserted topology section
>> "virtual_sites3"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "virtual_sites3" section to the right molecule.
>>
>> Do I have to have the virtual sites in the gro file also? This doesn't
>> make sense
>>
>
> Yes, you need their coordinates as part of the initial state.
>
> -Justin
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Justin A. Lemkul]

Gavin Melaugh wrote:

Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site  when I stated that it was to be at the
COG  of the  3 atoms in  the [virtual_sitesn] directive.



I believe this information is only used during mdrun to construct the position 
after forces have been applied and coordinates updated.  You can run a simple 
protein through pdb2gmx with -vsite hydrogens to see how all of this should be 
put together.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

O.k Cheers
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Yeah I see your point about the types. With regard to the initial
>> configuration state I would have assumed that gromacs knew the initial
>> position of the virtual site  when I stated that it was to be at the
>> COG  of the  3 atoms in  the [virtual_sitesn] directive.
>>
>
> I believe this information is only used during mdrun to construct the
> position after forces have been applied and coordinates updated.  You
> can run a simple protein through pdb2gmx with -vsite hydrogens to see
> how all of this should be put together.
>
> -Justin
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Mark Abraham]

On 6/05/2011 10:17 PM, Gavin Melaugh wrote:

Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site  when I stated that it was to be at the
COG  of the  3 atoms in  the [virtual_sitesn] directive.


Yes it does, but (IIRC) the implementation requires that each of the 
constructing atoms and the virtual atom(s) are distinct atoms. mdrun 
does the book-keeping to know which atoms are sensible at different 
stages of the integration. So the input coordinate file needs to have 
such atoms there, but I rather suspect their coordinates will get 
ignored - that's easily tested, of course.


Mark


Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Justin

I have tried this but I am now getting different errors. I take it that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?

Virtual sites are included in all the force fields already, but if you
want some custom name, then yes, include them in a new [atomtypes]
directive.  I see no reason to create three distinct, but identical,
types as you have.


I index the virtual sites in the atoms directive in accordance with the
rest of the molecule. atom numbers go from 1-228, therefore I label the
3 virtual sites 229 to231.
The error I get now is

Atom index (229) in virtual_sites3 out of bounds (1-228).
This probably means that you have inserted topology section
"virtual_sites3"
in a part belonging to a different molecule than you intended to.
In that case move the "virtual_sites3" section to the right molecule.

Do I have to have the virtual sites in the gro file also? This doesn't
make sense


Yes, you need their coordinates as part of the initial state.

-Justin



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Hi Mark

Cheers.Could you perhaps shed some insight into format of
[virtual_siten] when trying to define the VS at the COG of three atoms.
It is not obvious from the manual

Cheers

Gavin

Mark Abraham wrote:
> On 6/05/2011 10:17 PM, Gavin Melaugh wrote:
>> Yeah I see your point about the types. With regard to the initial
>> configuration state I would have assumed that gromacs knew the initial
>> position of the virtual site  when I stated that it was to be at the
>> COG  of the  3 atoms in  the [virtual_sitesn] directive.
>
> Yes it does, but (IIRC) the implementation requires that each of the
> constructing atoms and the virtual atom(s) are distinct atoms. mdrun
> does the book-keeping to know which atoms are sensible at different
> stages of the integration. So the input coordinate file needs to have
> such atoms there, but I rather suspect their coordinates will get
> ignored - that's easily tested, of course.
>
> Mark
>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Justin

 I have tried this but I am now getting different errors. I take it
 that:
 I specify the virtual sites in the atomtypes directive as I have seen
 from examples?
>>> Virtual sites are included in all the force fields already, but if you
>>> want some custom name, then yes, include them in a new [atomtypes]
>>> directive.  I see no reason to create three distinct, but identical,
>>> types as you have.
>>>
 I index the virtual sites in the atoms directive in accordance with
 the
 rest of the molecule. atom numbers go from 1-228, therefore I label
 the
 3 virtual sites 229 to231.
 The error I get now is

 Atom index (229) in virtual_sites3 out of bounds (1-228).
 This probably means that you have inserted topology section
 "virtual_sites3"
 in a part belonging to a different molecule than you intended to.
 In that case move the "virtual_sites3" section to the right molecule.

 Do I have to have the virtual sites in the gro file also? This doesn't
 make sense

>>> Yes, you need their coordinates as part of the initial state.
>>>
>>> -Justin
>>>
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Mark Abraham]

On 6/05/2011 10:39 PM, Gavin Melaugh wrote:

Hi Mark

Cheers.Could you perhaps shed some insight into format of
[virtual_siten] when trying to define the VS at the COG of three atoms.
It is not obvious from the manual


Indeed, it's undocumented - but I think Sikander's experience from my 
discussion in this thread earlier this month 
http://lists.gromacs.org/pipermail/gmx-users/2011-May/060994.html should 
point the way for you.


Mark


Cheers

Gavin

Mark Abraham wrote:

On 6/05/2011 10:17 PM, Gavin Melaugh wrote:

Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site  when I stated that it was to be at the
COG  of the  3 atoms in  the [virtual_sitesn] directive.

Yes it does, but (IIRC) the implementation requires that each of the
constructing atoms and the virtual atom(s) are distinct atoms. mdrun
does the book-keeping to know which atoms are sensible at different
stages of the integration. So the input coordinate file needs to have
such atoms there, but I rather suspect their coordinates will get
ignored - that's easily tested, of course.

Mark


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I have tried this but I am now getting different errors. I take it
that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?

Virtual sites are included in all the force fields already, but if you
want some custom name, then yes, include them in a new [atomtypes]
directive.  I see no reason to create three distinct, but identical,
types as you have.


I index the virtual sites in the atoms directive in accordance with
the
rest of the molecule. atom numbers go from 1-228, therefore I label
the
3 virtual sites 229 to231.
The error I get now is

Atom index (229) in virtual_sites3 out of bounds (1-228).
This probably means that you have inserted topology section
"virtual_sites3"
in a part belonging to a different molecule than you intended to.
In that case move the "virtual_sites3" section to the right molecule.

Do I have to have the virtual sites in the gro file also? This doesn't
make sense


Yes, you need their coordinates as part of the initial state.

-Justin



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Justin A. Lemkul]

Mark Abraham wrote:

On 6/05/2011 10:39 PM, Gavin Melaugh wrote:

Hi Mark

Cheers.Could you perhaps shed some insight into format of
[virtual_siten] when trying to define the VS at the COG of three atoms.
It is not obvious from the manual


Indeed, it's undocumented - but I think Sikander's experience from my 
discussion in this thread earlier this month 
http://lists.gromacs.org/pipermail/gmx-users/2011-May/060994.html should 
point the way for you.




I've filed a redmine issue for this (http://redmine.gromacs.org/issues/748); it 
looks like the organization of [virtual_sitesn] is different from the other 
[virtual_sites*] directives in terms of the contents.  I think this is why there 
was a "type 7" being detected before.


-Justin


Mark


Cheers

Gavin

Mark Abraham wrote:

On 6/05/2011 10:17 PM, Gavin Melaugh wrote:

Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site  when I stated that it was to be at the
COG  of the  3 atoms in  the [virtual_sitesn] directive.

Yes it does, but (IIRC) the implementation requires that each of the
constructing atoms and the virtual atom(s) are distinct atoms. mdrun
does the book-keeping to know which atoms are sensible at different
stages of the integration. So the input coordinate file needs to have
such atoms there, but I rather suspect their coordinates will get
ignored - that's easily tested, of course.

Mark


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I have tried this but I am now getting different errors. I take it
that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?

Virtual sites are included in all the force fields already, but if you
want some custom name, then yes, include them in a new [atomtypes]
directive.  I see no reason to create three distinct, but identical,
types as you have.


I index the virtual sites in the atoms directive in accordance with
the
rest of the molecule. atom numbers go from 1-228, therefore I label
the
3 virtual sites 229 to231.
The error I get now is

Atom index (229) in virtual_sites3 out of bounds (1-228).
This probably means that you have inserted topology section
"virtual_sites3"
in a part belonging to a different molecule than you intended to.
In that case move the "virtual_sites3" section to the right molecule.

Do I have to have the virtual sites in the gro file also? This 
doesn't

make sense


Yes, you need their coordinates as part of the initial state.

-Justin





--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Hi Mark

Many thanks to you and all your colleagues for replying. This has
worked, at least there are now no errors. Where the manual is incorrect
is that it leads you to believe that you state;
[virtual _siten]
;index of VS  index of atoms for COG  func
229 8 11 151

However the function type should be stated before the atom indices
comprising the COG
;index of VS  func indices
   229  1   8 11 15 

Cheers

Gavin

Mark Abraham wrote:
> On 6/05/2011 10:39 PM, Gavin Melaugh wrote:
>> Hi Mark
>>
>> Cheers.Could you perhaps shed some insight into format of
>> [virtual_siten] when trying to define the VS at the COG of three atoms.
>> It is not obvious from the manual
>
> Indeed, it's undocumented - but I think Sikander's experience from my
> discussion in this thread earlier this month
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/060994.html
> should point the way for you.
>
> Mark
>
>> Cheers
>>
>> Gavin
>>
>> Mark Abraham wrote:
>>> On 6/05/2011 10:17 PM, Gavin Melaugh wrote:
 Yeah I see your point about the types. With regard to the initial
 configuration state I would have assumed that gromacs knew the initial
 position of the virtual site  when I stated that it was to be at the
 COG  of the  3 atoms in  the [virtual_sitesn] directive.
>>> Yes it does, but (IIRC) the implementation requires that each of the
>>> constructing atoms and the virtual atom(s) are distinct atoms. mdrun
>>> does the book-keeping to know which atoms are sensible at different
>>> stages of the integration. So the input coordinate file needs to have
>>> such atoms there, but I rather suspect their coordinates will get
>>> ignored - that's easily tested, of course.
>>>
>>> Mark
>>>
 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Justin
>>
>> I have tried this but I am now getting different errors. I take it
>> that:
>> I specify the virtual sites in the atomtypes directive as I have
>> seen
>> from examples?
> Virtual sites are included in all the force fields already, but if
> you
> want some custom name, then yes, include them in a new [atomtypes]
> directive.  I see no reason to create three distinct, but identical,
> types as you have.
>
>> I index the virtual sites in the atoms directive in accordance with
>> the
>> rest of the molecule. atom numbers go from 1-228, therefore I label
>> the
>> 3 virtual sites 229 to231.
>> The error I get now is
>>
>> Atom index (229) in virtual_sites3 out of bounds (1-228).
>> This probably means that you have inserted topology section
>> "virtual_sites3"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "virtual_sites3" section to the right
>> molecule.
>>
>> Do I have to have the virtual sites in the gro file also? This
>> doesn't
>> make sense
>>
> Yes, you need their coordinates as part of the initial state.
>
> -Justin
>
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Am I correct in saying now, from the following topology (exerpts), that
the virtual site VS will only interact with C3?
I guess I don't have to give the atom indices of this interaction in the
pair list which I use only for 1_4 interactions?
Can I use sigma and epsilon in the nonbond_params directive like in
atomtypes.

;Parameter level
[defaults]
; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
 1 3  yes0.5 0.5

[atomtypes]
;type mass   charge  ptype sigma(nm)
epsilon(kjmol-1)
   CB 12.011000  0.00   A  0.355000  0.292880
   CA 12.011000 -0.115000   A  0.355000  0.292880
   HC  1.008000  0.115000   A  0.242000  0.125520
   CU 13.019000  0.265000   A  0.35  0.334720
   NU 14.007000 -0.597000   A  0.325000  0.711280
   CH 13.019000  0.332000   A  0.385000  0.334720
   C3 15.035000  0.00   A  0.390500  0.732200
   C2 14.027000  0.00   A  0.390500  0.493712
   VS  0.0   0.0V  0.0   0.0


[nonbond_params]
;ij  func sigmaepsilon
VS   C31   0.1 0.03153

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjorder not working

[shivangi nangia]

Thanks Justin, that was helpful.

I have a following question.

Since in my system I have both methanol and water and I want to order both
of them ( my eventual aim to make a sphere), is there is way to override -na
option ( for water na 4, methanol 3).
Is there is way that all the components of the system get ordered with
respect to the protein?

or I have have to play around ordering them one by one?

Thanks,
SN


On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul  wrote:

>
>
> shivangi nangia wrote:
>
>> Hello,
>>
>> Came back to the set of calculations I was doing few days back.
>>
>> I have a box of water (TIP4P), methanol, protein and DHB anions.
>>
>> I minimized this system.
>>
>> Trying to use trjorder for water molecules with respect to the protein
>> (eventually I want to make a sphere by ordering and getting rid of the
>> molecules I do not want)
>>
>> In the index.ndx file i specified atom "144" (belongs to protein)
>>
>> so when I run
>>
>>  trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro
>>
>> I pick number associated with atom "144" and SOL ( tip4p water) and I
>> generate ordered.gro
>>
>> The sequence for SOL changes ( random), but when I use g_dist as I go down
>> the ordered.gro, there is still no trend ( ascending with respect to
>> protein)
>>
>>
>>
> I suspect your index file is wrong.  Presumably, you have measured
> distances to individual water molecules using g_dist, which would require a
> custom index group for each water molecule analyzed, correct?  If you use
> ordered.gro, the residue numbers will indeed be scrambled based on ordering,
> but the distance will correspond to the original distance, not the ordered
> one.
>
> The solution is to use your unordered coordinate file or .tpr file to
> create the index group, then perform the distance measurements.
>  Alternatively, use genconf to renumber ordered.gro to get sequential
> residue numbers, then create whatever index file you might need from the
> renumbered coordinate file.
>
>
>
>>
>>
>> Also, -da 0 refers to an atom OR COM of the molecule.
>> using   trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o
>> ordered.gro and running it
>>
>> and choosing "1" for protein and "14" for SOL means that gromacs
>> automatically understands that protein's COM is to be used to order SOL
>> (tip4p, -na 4) ??
>>
>>
> As the documentation is written, yes.
>
>
>  If so, then tha talso generates a .gro file which produces random water
>> molecules but there is again no trend.
>>
>>
> Same problem as above, I suspect.
>
> -Justin
>
>  I am very confused about using trjorder, it will be really helpful if
>> someone or Mark can help me understand.
>>
>> Thanks a lot
>> SN
>>
>>
>> On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>On 4/29/2011 11:29 AM, shivangi nangia wrote:
>>
>>>Hello,
>>>
>>>The manual explaining trjorder says:
>>>
>>>trjorder orders molecules according to the smallest distance to
>>>atoms in a reference group or on z-coordinate (with option -z).
>>>With distance ordering, it will ask for a group of reference atoms
>>>and a group of molecules. For each frame of the trajectory the
>>>selected molecules will be reordered according to the shortest
>>>distance between atom number -da in the molecule and all the atoms
>>>in the reference group. *The center of mass of the molecules can
>>>be used instead of a reference atom by setting -da to 0*
>>>
>>>In order to arrange water molecules in accordance with the COM of
>>>the polypeptide, I chose -da 0.
>>>
>>
>>As it says above, -da refers to an atom or COM of the molecule, not
>>the reference group. This could be worded better in the documentation.
>>
>>Be sure you're choosing the groups you think you are choosing - you
>>not copying relevant parts of your terminal output into emails is
>>making things difficult.
>>
>>Mark
>>
>>
>>>Am I wrong?
>>>
>>>Thanks,
>>>SN
>>>
>>>
>>>
>>>
>>>On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham
>>>mailto:mark.abra...@anu.edu.au>> wrote:
>>>
>>>On 4/29/2011 4:08 AM, shivangi nangia wrote:
>>>
>>>Hello all,
>>>
>>>I am trying to order the TIP4P water molecules in my
>>>system with respect to the polypeptide in my system.
>>>
>>>The command I am using is:
>>>
>>> trjorder -f shape.gro -s shape.tpr -da 0  -na 4 -o
>>>ordered.gro
>>>
>>>This runs without any error and ordered.gro is generated
>>>with random sequence of water molecules.
>>>
>>>Just to cross check I calculated the distances between one
>>>of atoms of the polypeptide and oxyegn atom of different
>>>"ordered" water molecules.
>>>I found, there is no ascendig trend in the distances with
>>>respect to the polypeptide as a go down in the
>>>"ordered.gro" file.
>>

Re: [gmx-users] trjorder not working

[Justin A. Lemkul]

shivangi nangia wrote:

Thanks Justin, that was helpful.

I have a following question.

Since in my system I have both methanol and water and I want to order 
both of them ( my eventual aim to make a sphere), is there is way to 
override -na option ( for water na 4, methanol 3).
Is there is way that all the components of the system get ordered with 
respect to the protein?




If they all have different numbers of atoms, no.


or I have have to play around ordering them one by one?



Probably.  If your goal is to set up a spherical system, there are probably far 
easier ways to do this with genbox -shell and/or VMD/NAMD solvation procedures 
to build spheres.


-Justin


Thanks,
SN


On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul > wrote:




shivangi nangia wrote:

Hello,

Came back to the set of calculations I was doing few days back.

I have a box of water (TIP4P), methanol, protein and DHB anions.

I minimized this system.

Trying to use trjorder for water molecules with respect to the
protein (eventually I want to make a sphere by ordering and
getting rid of the molecules I do not want)

In the index.ndx file i specified atom "144" (belongs to protein)

so when I run

 trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro

I pick number associated with atom "144" and SOL ( tip4p water)
and I generate ordered.gro

The sequence for SOL changes ( random), but when I use g_dist as
I go down the ordered.gro, there is still no trend ( ascending
with respect to protein)



I suspect your index file is wrong.  Presumably, you have measured
distances to individual water molecules using g_dist, which would
require a custom index group for each water molecule analyzed,
correct?  If you use ordered.gro, the residue numbers will indeed be
scrambled based on ordering, but the distance will correspond to the
original distance, not the ordered one.

The solution is to use your unordered coordinate file or .tpr file
to create the index group, then perform the distance measurements.
 Alternatively, use genconf to renumber ordered.gro to get
sequential residue numbers, then create whatever index file you
might need from the renumbered coordinate file.





Also, -da 0 refers to an atom OR COM of the molecule.
using   trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o
ordered.gro and running it

and choosing "1" for protein and "14" for SOL means that gromacs
automatically understands that protein's COM is to be used to
order SOL (tip4p, -na 4) ??


As the documentation is written, yes.


If so, then tha talso generates a .gro file which produces
random water molecules but there is again no trend.


Same problem as above, I suspect.

-Justin

I am very confused about using trjorder, it will be really
helpful if someone or Mark can help me understand.

Thanks a lot
SN


On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 4/29/2011 11:29 AM, shivangi nangia wrote:

   Hello,

   The manual explaining trjorder says:

   trjorder orders molecules according to the smallest
distance to
   atoms in a reference group or on z-coordinate (with
option -z).
   With distance ordering, it will ask for a group of
reference atoms
   and a group of molecules. For each frame of the
trajectory the
   selected molecules will be reordered according to the
shortest
   distance between atom number -da in the molecule and all
the atoms
   in the reference group. *The center of mass of the
molecules can
   be used instead of a reference atom by setting -da to 0*

   In order to arrange water molecules in accordance with
the COM of
   the polypeptide, I chose -da 0.


   As it says above, -da refers to an atom or COM of the
molecule, not
   the reference group. This could be worded better in the
documentation.

   Be sure you're choosing the groups you think you are choosing
- you
   not copying relevant parts of your terminal output into emails is
   making things difficult.

   Mark


   Am I wrong?

   Thanks,
   SN




   On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham
   mailto:mark.abra...@anu.edu.au>
>> wrote:

   O

[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load)

[J. Nathan Scott]

Oops, this message and the original should have gone to the VMD mailing list
and not Gromacs of course. My mistake, apologies for cluttering your inbox.
:-)

-Nathan

On Thu, May 5, 2011 at 3:35 PM, J. Nathan Scott <
scot...@chemistry.montana.edu> wrote:

> Hello again, fellow gmx-users,
>
> I finally found my coding error that only set the User data for the first
> half of the frames loaded, it was a simple indexing error after all.
> However, I would still *greatly* appreciate any assistance with speeding up
> the following loop:
>
>
> for {set k 6} {$k <= 141} {incr k} {
> set prot [atomselect $mol_ID "resid $k" frame $j]
> set num [$prot num]
> $prot frame $j
> set user_list {}
> set u [lindex $efield [expr $k - 6]]
> for {set b 1} {$b <= $num} {incr b} {
>lappend user_list $u
> }
> $prot set user $user_list
> $prot delete
> }
>
> Is there a simpler way to accomplish the task of assigning a single User
> value to individual residues without first atomselecting each one, getting
> its number of atoms, and then finally looping over the atoms to build a
> user_list? I'm hoping that there is some better way to do this that I
> haven't thought of yet. My script runs very wonderfully except for this
> chunk.
>
> Thanks in advance for any help you can provide,
>
> -Nathan
>
>
> On Wed, May 4, 2011 at 11:06 AM, J. Nathan Scott <
> scot...@chemistry.montana.edu> wrote:
>
>> Hello all,
>>
>> I have written a script that does per-time-step coloring of the water
>> molecules, residues, and ions in my protein based on electric field values I
>> previously calculated. I received excellent help here a few months sorting
>> out some problems with the script, but there is one big one remaining that I
>> hope someone can help with.
>>
>> The problem is that only half the frames (the first half) in my simulation
>> are getting colored, and I can't figure out why. This happens no matter how
>> many frames I load, whether the full trajectory or just a few hundred
>> frames. For what it's worth, the machine I'm running on has 12 GB of RAM, a
>> very nice video card, and a new Xeon quad core processor, so I don't think
>> this is an issue of system resources. At least I can see that there is still
>> tons of free RAM when I am experiencing this issue.
>>
>> Also, I would sincerely appreciate any advice on speeding up one of my
>> loops. To color the water molecules and ions I can simply atomselect them
>> all, and then loop through the values from the electric field data file for
>> that timestep and assign the color value to a user list either 3 or 1 times
>> respectively to color each atom.
>>
>> However, for the residues in the protein I am having to atomselect them
>> one at a time, get the number of atoms for that residue, and then do another
>> loop to build a list of the correct length to assign the user values to each
>> atom of the residue. Can anyone recommend a more efficient way of coloring
>> the residues? When the residue coloring part of the script is stripped out
>> it runs so much faster despite the fact that there are far fewer protein
>> atoms than there are water or ion atoms, so I know this method of assignment
>> is sluggish.
>>
>> Please see the script below my signature, and thank you in advance for any
>> advice you can provide.
>>
>> --
>> --
>> J. Nathan Scott, Ph.D.
>> Postdoctoral Fellow
>> Department of Chemistry and Biochemistry
>> Montana State University
>>
>>
>>
>>
>> ###
>> set first 0;
>> set last 1000;
>> set mut wt;
>> set mut_ wt_;
>> set i $first; #i will be timestep/filename indicator,
>> set j 0;
>>
>> mol new /data/1stn/xtc/1stn_$mut.gro type gro waitfor all
>> mol addfile /data/1stn/xtc/1stn_$mut.xtc type xtc waitfor all first $first
>> last $l$
>> set mol_ID top;
>> set n [ molinfo $mol_ID get numframes ];
>> animate goto 0
>> animate delete  beg 0 end 0 skip 0 0
>> mol delrep 0 $mol_ID
>>
>> while {$i <= $last} {
>> set fp [open "/data/1stn/$mut/pd5/pd5.stripped/1stn_$mut_$i.pd5"
>> r]
>> set file_data [read $fp]
>> close $fp
>>
>> set data [split $file_data "\n"]
>> foreach {one} $data {
>> lappend efield [lindex $one 3]
>> }
>>
>> ### Looping through residues in the for loop,
>> ### selecting one residue at a time, getting its number of atoms,
>> ### and then building a user value list for each of those
>> ### atoms in another for loop.
>>
>> for {set k 6} {$k <= 141} {incr k} {
>> set prot [atomselect $mol_ID "resid $k" frame $j]
>> set num [$prot num]
>> $prot frame $j
>> set user_list {}
>> set u [lindex $efield [expr $k - 6]]
>> for {set b 1} {$b <= $num} {incr b} {
>>lappend user_list $u
>> }
>> $prot set user $user_list
>> $prot delete
>>

Re: [gmx-users] trjconv center on protein

[Tomek Wlodarski]

Dear Justin,

Thanks, sure I will give more details.

This command I've used for trajectory conversion:

trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr

Then I was analysing a new and old trajectory in VMD with my own script.
I have noticed that in old trajectory water234 between frame 0 and 1
moves 1.2089872880760837 A, whereas the same water molecule between
the same frames but in the new trajectory moves 1.4933788404331632 A
I check different water - water236 and situation was similar: old
trajectory -> 0.6436778227352694 A and in new trajectory it was
0.2921395545132566 A

So after trajectory conversion water displacement is different,
sometimes in the new trajectory is bigger and sometimes is smaller
that it was in old one...

I used the same conversion for part of my simulation where protein was
in the center of the system, and results were similar.

I believe is not problem with my vmd script because even when I open
in the same window new and old trajectory in VMD I can see "by eye"
the difference of water movement
I am missing something?
Thanks for any suggestions and help!

Best!

tomek

On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul  wrote:
>
>
> Tomek Wlodarski wrote:
>>
>> Hi all!
>>
>> I have a trajectory of simulation (protein in box of water) and I
>> would like to have all the time protein in the center of the water
>> box, becasue protein is drifting to the edge during simulation and I
>> am calculating some properties of water arround the protein.
>> I was playing with trjconv and -pbc and -center options and I menage
>> to do what I wanted, however there was something bizarre for me or
>> maybe I do not fully understand how this centering works
>> I noticed that the same water molecule traverse different distance
>> between the same frames of simulation in the original than in
>> converted trajectory...
>> Why and how it is possible?
>> Thank you for any suggestions and help!
>
> Without seeing the exact command(s) you used to produce the centered
> trajectory, especially if it was a combination of some -pbc method and
> -center, then it's impossible to say for certain.  I'd venture a guess that
> you've simply managed to "correct" for water molecules jumping across
> boundaries or something, but that's just a guess, and without actual
> commands and the output you are obtaining, there's not much more to offer
> beyond speculation.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv center on protein

[Justin A. Lemkul]

Tomek Wlodarski wrote:

Dear Justin,

Thanks, sure I will give more details.

This command I've used for trajectory conversion:

trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr

Then I was analysing a new and old trajectory in VMD with my own script.
I have noticed that in old trajectory water234 between frame 0 and 1
moves 1.2089872880760837 A, whereas the same water molecule between
the same frames but in the new trajectory moves 1.4933788404331632 A
I check different water - water236 and situation was similar: old
trajectory -> 0.6436778227352694 A and in new trajectory it was
0.2921395545132566 A

So after trajectory conversion water displacement is different,
sometimes in the new trajectory is bigger and sometimes is smaller
that it was in old one...

I used the same conversion for part of my simulation where protein was
in the center of the system, and results were similar.

I believe is not problem with my vmd script because even when I open
in the same window new and old trajectory in VMD I can see "by eye"
the difference of water movement
I am missing something?
Thanks for any suggestions and help!



Are all the measurements being done in VMD, or are you using g_dist for any of 
these?  If you're using g_dist, then some of the distances may be affected by 
using your old .tpr file, wherein the protein is perhaps not centered.


If all of the measurements are being done in VMD, then I can't comment, but 
perhaps someone else can.  It might be useful to show how you're doing these 
measurements.  If you're not using g_dist, it would be interesting to see how 
the results of g_dist and VMD compare, in order to tease out the source of the 
difference.


-Justin


Best!

tomek

On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul  wrote:


Tomek Wlodarski wrote:

Hi all!

I have a trajectory of simulation (protein in box of water) and I
would like to have all the time protein in the center of the water
box, becasue protein is drifting to the edge during simulation and I
am calculating some properties of water arround the protein.
I was playing with trjconv and -pbc and -center options and I menage
to do what I wanted, however there was something bizarre for me or
maybe I do not fully understand how this centering works
I noticed that the same water molecule traverse different distance
between the same frames of simulation in the original than in
converted trajectory...
Why and how it is possible?
Thank you for any suggestions and help!

Without seeing the exact command(s) you used to produce the centered
trajectory, especially if it was a combination of some -pbc method and
-center, then it's impossible to say for certain.  I'd venture a guess that
you've simply managed to "correct" for water molecules jumping across
boundaries or something, but that's just a guess, and without actual
commands and the output you are obtaining, there's not much more to offer
beyond speculation.

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists





--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Sikandar Mashayak]

Yes, since sigma and epsilon are zero for VS then interactions between and
VS-VS and VS-(any other atom) would result in zero force. Since you
explicitly define the interaction between VS-C3, combination rule won't be
used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3)
epsilon(VS_C3) you defined under [nonbond_params]

cheers

sikandar

On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh  wrote:

> Am I correct in saying now, from the following topology (exerpts), that
> the virtual site VS will only interact with C3?
> I guess I don't have to give the atom indices of this interaction in the
> pair list which I use only for 1_4 interactions?
> Can I use sigma and epsilon in the nonbond_params directive like in
> atomtypes.
>
> ;Parameter level
> [defaults]
> ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
> 1 3  yes0.5 0.5
>
> [atomtypes]
> ;type mass   charge  ptype sigma(nm)
> epsilon(kjmol-1)
>   CB 12.011000  0.00   A  0.355000  0.292880
>   CA 12.011000 -0.115000   A  0.355000  0.292880
>HC  1.008000  0.115000   A  0.242000  0.125520
>   CU 13.019000  0.265000   A  0.35  0.334720
>   NU 14.007000 -0.597000   A  0.325000  0.711280
>   CH 13.019000  0.332000   A  0.385000  0.334720
>   C3 15.035000  0.00   A  0.390500  0.732200
>   C2 14.027000  0.00   A  0.390500  0.493712
>   VS  0.0   0.0V  0.0   0.0
>
>
> [nonbond_params]
> ;ij  func sigmaepsilon
> VS   C31   0.1 0.03153
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

Cheers Sikandar

I take it that because combination rule 3 (provide sigma and epsilon) is
stated gromacs assumes that all values in nonbonding parameters are
sigma and epsilon. I know this tp be tru for the atomtypes but does it
filter down to all intermolecular interactions.

Cheers

Gavin

Sikandar Mashayak wrote:
> Yes, since sigma and epsilon are zero for VS then interactions between
> and VS-VS and VS-(any other atom) would result in zero force. Since
> you explicitly define the interaction between VS-C3, combination rule
> won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per
> sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params]
>
> cheers
>
> sikandar
>
> On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh  > wrote:
>
> Am I correct in saying now, from the following topology (exerpts),
> that
> the virtual site VS will only interact with C3?
> I guess I don't have to give the atom indices of this interaction
> in the
> pair list which I use only for 1_4 interactions?
> Can I use sigma and epsilon in the nonbond_params directive like in
> atomtypes.
>
> ;Parameter level
> [defaults]
> ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
> 1 3  yes0.5 0.5
>
> [atomtypes]
> ;type mass   charge  ptype sigma(nm)
> epsilon(kjmol-1)
>   CB 12.011000  0.00   A  0.355000  0.292880
>   CA 12.011000 -0.115000   A  0.355000  0.292880
>   HC  1.008000  0.115000   A  0.242000  0.125520
>   CU 13.019000  0.265000   A  0.35  0.334720
>   NU 14.007000 -0.597000   A  0.325000  0.711280
>   CH 13.019000  0.332000   A  0.385000  0.334720
>   C3 15.035000  0.00   A  0.390500  0.732200
>   C2 14.027000  0.00   A  0.390500  0.493712
>   VS  0.0   0.0V  0.0   0.0
>
>
> [nonbond_params]
> ;ij  func sigmaepsilon
> VS   C31   0.1 0.03153
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> 
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
> .
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] "No molecules were defined in the system"

[Maria Hamilton]

Hi all

I got .itp and .pdb files of sulfate ion from PRODRG. I add it as an extra
molecule (in genbox using -ci) my simulation box. I can see it visaully by
VMD in my system. but it is not in topol.top and when I want run my program
I receive the following error:

"No molecules were defined in the system"

The name of .itp file, its inclusion in topol.top are the same.

Would you please help me?What should I do?


Thanks alot

Maria
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: "No molecules were defined in the system"

[Vitaly Chaban]

>
> I got .itp and .pdb files of sulfate ion from PRODRG. I add it as an extra
> molecule (in genbox using -ci) my simulation box. I can see it visaully by
> VMD in my system. but it is not in topol.top and when I want run my program
> I receive the following error:
>
> "No molecules were defined in the system"
>
> The name of .itp file, its inclusion in topol.top are the same.
>


Show us your "[ system ]" subsection of the topology.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] The problem of .trr file size limit?

[gromacs564]

Hello, everyone
 I submit a job with gromacs-4.5.4 in cluster ,but the md.trr file can not  
write if the file size more than 17247,252,480K(about 16.06G)?
and the program always output :"Cannot write trajectory frame; maybe you 
are out of quota?" There is sufficient disk space,and the system is redhat 64. 
Could you give me some solutions? Thanks! 
 

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] The problem of .trr file size limit?

[Matthew Zwier]

The filesystem you're storing on may not allow single files larger
than 16.0 GB.  What filesystem are you using?  ext3?

Also, do you really need to write such a large TRR file?  Can you
store to the TRR file less frequently (for restarts, etc) and store to
XTC instead?  You'll get *much* more information stored in the same
amount of space that way.

Matt Z.

2011/5/6 gromacs564 :
> Hello, everyone
>  I submit a job with gromacs-4.5.4 in cluster ,but the md.trr file can
> not  write if the file size more than 17247,252,480K(about 16.06G)?
>     and the program always output :"Cannot write trajectory frame; maybe you
> are out of quota?" There is sufficient disk space,and the system is redhat
> 64. Could you give me some solutions? Thanks!
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] trjconv center on protein

[Tsjerk Wassenaar]

Hey :)

Option -center shifts the system, which will show up as a component in the
displacement.

Cheers,

Tsjerk

On May 6, 2011 5:39 PM, "Justin A. Lemkul"  wrote:

Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more
details. > > This comman...
Are all the measurements being done in VMD, or are you using g_dist for any
of these?  If you're using g_dist, then some of the distances may be
affected by using your old .tpr file, wherein the protein is perhaps not
centered.

If all of the measurements are being done in VMD, then I can't comment, but
perhaps someone else can.  It might be useful to show how you're doing these
measurements.  If you're not using g_dist, it would be interesting to see
how the results of g_dist and VMD compare, in order to tease out the source
of the difference.

-Justin

> Best! > > tomek > > On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul <
jalem...@vt.edu> wrote: >>...
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] virtual sites set up for topology file

[Sikandar Mashayak]

yes it will...

On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh  wrote:

> Cheers Sikandar
>
> I take it that because combination rule 3 (provide sigma and epsilon) is
> stated gromacs assumes that all values in nonbonding parameters are
> sigma and epsilon. I know this tp be tru for the atomtypes but does it
> filter down to all intermolecular interactions.
>
> Cheers
>
> Gavin
>
> Sikandar Mashayak wrote:
> > Yes, since sigma and epsilon are zero for VS then interactions between
> > and VS-VS and VS-(any other atom) would result in zero force. Since
> > you explicitly define the interaction between VS-C3, combination rule
> > won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per
> > sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params]
> >
> > cheers
> >
> > sikandar
> >
> > On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh  > > wrote:
> >
> > Am I correct in saying now, from the following topology (exerpts),
> > that
> > the virtual site VS will only interact with C3?
> > I guess I don't have to give the atom indices of this interaction
> > in the
> > pair list which I use only for 1_4 interactions?
> > Can I use sigma and epsilon in the nonbond_params directive like in
> > atomtypes.
> >
> > ;Parameter level
> > [defaults]
> > ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
> > 1 3  yes0.5 0.5
> >
> > [atomtypes]
> > ;type mass   charge  ptype sigma(nm)
> > epsilon(kjmol-1)
> >   CB 12.011000  0.00   A  0.355000  0.292880
> >   CA 12.011000 -0.115000   A  0.355000  0.292880
> >   HC  1.008000  0.115000   A  0.242000  0.125520
> >   CU 13.019000  0.265000   A  0.35  0.334720
> >   NU 14.007000 -0.597000   A  0.325000  0.711280
> >   CH 13.019000  0.332000   A  0.385000  0.334720
> >   C3 15.035000  0.00   A  0.390500  0.732200
> >   C2 14.027000  0.00   A  0.390500  0.493712
> >   VS  0.0   0.0V  0.0   0.0
> >
> >
> > [nonbond_params]
> > ;ij  func sigmaepsilon
> > VS   C31   0.1 0.03153
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > 
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org
> > .
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] using tcl to scipt gromacs

[jeremy adler]

I like to use tcl as my scripting language and after much pain and
tribulation i have figured out how to get it to call gromacs without raising
an error. Use exec -ignorestderr g_yourfavoritegromacsfunction. Note this
will only work with versions of tcl 8.5 and later so if you use and older
version (default if youre on ubuntu) and like using tcl than update it if
you want to use it to call gromacs.

Jeremy
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] ambar to opls force field

[Nilesh Dhumal]

Hello,

How can I convert ambar force field to opls force field.

Should I half the force constant of bond (Ka)  and angle (Kb)?


NIlesh




-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] ambar to opls force field

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

How can I convert ambar force field to opls force field.

Should I half the force constant of bond (Ka)  and angle (Kb)?



Why would you do that?  Most of the bonded parameters in OPLS were taken from 
AMBER directly, IIRC.  If you need to parameterize some new bonded parameters, 
you'd be better served deriving them in a way that is compatible with the modern 
OPLS-AA force field (probably QM/geometry optimization), rather than trying to 
hack something together.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] ambar to opls force field

[Mark Abraham]

On 7/05/2011 8:10 AM, Nilesh Dhumal wrote:

Hello,

How can I convert ambar force field to opls force field.

Should I half the force constant of bond (Ka)  and angle (Kb)?


Having read the papers describing how their bonded interactions work, 
shouldn't you know how to convert them?


Having a good reason for mixing force fields, would help, too...

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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] different number of waters (grompp)

[Ricardo O. S. Soares]

Hello dear users,

I'm having a problem trying to simulate one trimer. I'm using tip4p water and 
right after I fill the box with water and try to pre-process (grompp) the 
resulting .gro and .top, I get the following error: 



---
Program grompp, VERSION 4.5.1
Source code file: grompp.c, line: 377

Fatal error:
number of coordinates in coordinate file (../box/box_water.gro, 274045)
 does not match topology (../top_water.top, 273029)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Here's the ending of the .top file:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_H 1
Protein_chain_L 1
SOL59
SOL97
SOL98
SOL 66032

And the beginning of the .gro file shows the number "274045"

Thanks for your time.

Ricardo.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] different number of waters (grompp)

[Justin A. Lemkul]

Ricardo O. S. Soares wrote:

Hello dear users,

I'm having a problem trying to simulate one trimer. I'm using tip4p 
water and right after I fill the box with water and try to pre-process 
(grompp) the resulting .gro and .top, I get the following error:



---
Program grompp, VERSION 4.5.1
Source code file: grompp.c, line: 377

Fatal error:
number of coordinates in coordinate file (../box/box_water.gro, 274045)
 does not match topology (../top_water.top, 273029)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Here's the ending of the .top file:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_H 1
Protein_chain_L 1
SOL59
SOL97
SOL98
SOL 66032

And the beginning of the .gro file shows the number "274045"



The .top specifies fewer atoms than the .gro, so it's possible that there was 
some problem when genbox wrote the topology.  The screen output of genbox should 
have indicated how many waters were added - does this number match what you see 
in the .top?  Presumably the first three SOL entries are crystal waters?  I 
don't know that pre-existing waters should cause any problem, but it's possible. 
 The difference in the number of atoms is 1016, or 254 TIP4P molecules. 
Coincidentally, 59 + 97 + 98 = 254.  It looks like genbox wrote the wrong number 
 of molecules it added.  If this is the case, please file an issue on 
redmine.gromacs.org with the exact steps taken to reproduce the problem so it 
can be fixed.


-Justin


Thanks for your time.

Ricardo.



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] different number of waters (grompp)

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Ricardo O. S. Soares wrote:

Hello dear users,

I'm having a problem trying to simulate one trimer. I'm using tip4p 
water and right after I fill the box with water and try to pre-process 
(grompp) the resulting .gro and .top, I get the following error:



---
Program grompp, VERSION 4.5.1
Source code file: grompp.c, line: 377

Fatal error:
number of coordinates in coordinate file (../box/box_water.gro, 274045)
 does not match topology (../top_water.top, 273029)
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---

Here's the ending of the .top file:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_H 1
Protein_chain_L 1
SOL59
SOL97
SOL98
SOL 66032

And the beginning of the .gro file shows the number "274045"



The .top specifies fewer atoms than the .gro, so it's possible that 
there was some problem when genbox wrote the topology.  The screen 
output of genbox should have indicated how many waters were added - does 
this number match what you see in the .top?  Presumably the first three 
SOL entries are crystal waters?  I don't know that pre-existing waters 
should cause any problem, but it's possible.  The difference in the 
number of atoms is 1016, or 254 TIP4P molecules. Coincidentally, 59 + 97 
+ 98 = 254.  It looks like genbox wrote the wrong number  of molecules 
it added.  If this is the case, please file an issue on 
redmine.gromacs.org with the exact steps taken to reproduce the problem 
so it can be fixed.




I just noticed you're using version 4.5.1, so you should upgrade to 4.5.4 and 
see if the issue persists before filing any report.  Debugging outdated versions 
which may have already been fixed is not terribly productive :)


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Using the XTC library

[Ryan S Davis (rsdavis1)]

I am trying to use the XTC library in my code but I am just not good at this 
stuff.
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library


I installed using
./configure --prefix=/$HOME/apps/xdrfile
make install

everything seemed to go well and the make check said everything passed.

So then I try a test code

  1 #include 
  2 #include "xdrfile_xtc.h"
  3 using namespace std;
  4 
  5 int main()
  6 {
  7 
  8  int natoms;
  9  read_xtc_natoms("traj.xtc", &natoms);
 10 return 0;
 11 }

and I compile with

icc  -I/$HOME/apps/xdrfile/include/xdrfile  -L/$HOME/apps/xdrfile/lib/  test.cpp

and i get an error saying...

undefined reference to 'read_xtc_natoms(char *, int*)'

I am sure that I am doing something stupid. I tried a C compiler and linking to 
few other random places but, like I said, this stuff (installing libraries and 
linking) is new to me.
Please help.

Thanks
Ryan--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Using the XTC library

[Mark Abraham]

On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:

I am trying to use the XTC library in my code but I am just not good at this 
stuff.
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library


I installed using
./configure --prefix=/$HOME/apps/xdrfile


This might not be the problem, but the HOME environment variable here 
and below will normally start with a slash, and so you should not 
preface it with another.



make install

everything seemed to go well and the make check said everything passed.

So then I try a test code

   1 #include
   2 #include "xdrfile_xtc.h"
   3 using namespace std;
   4
   5 int main()
   6 {
   7
   8  int natoms;
   9  read_xtc_natoms("traj.xtc",&natoms);
  10 return 0;
  11 }

and I compile with

icc  -I/$HOME/apps/xdrfile/include/xdrfile  -L/$HOME/apps/xdrfile/lib/  test.cpp

and i get an error saying...

undefined reference to 'read_xtc_natoms(char *, int*)'

I am sure that I am doing something stupid. I tried a C compiler and linking to 
few other random places but, like I said, this stuff (installing libraries and 
linking) is new to me.
Please help.


icc  -I$HOME/apps/xdrfile/include/xdrfile test.cpp

will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h

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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_sas query

[Anirban Ghosh]

Hi ALL,

I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms as calculation group and Protein as the output group. So I
need to make a group with Protein+Lipid+Ions as the calculation group.
Right?
Thanks a lot in advance.

Regards,

Anirban
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Using the XTC library

[Joshua L. Phillips]

You will need to link with the library as well (-lxdrfile)

Something like the following should work (if the paths that you provided
are correct):

icpc -I$HOME/apps/xdrfile/include/xdrfile \
 -L$HOME/apps/xdrfile/lib test.cpp -o test -lxdrfile

(Since, this is C++ code, then you should be using icpc instead of
icc...)

-- Josh

On Sat, 2011-05-07 at 13:55 +1000, Mark Abraham wrote:
> On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:
> > I am trying to use the XTC library in my code but I am just not good at 
> > this stuff.
> > http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
> >
> >
> > I installed using
> > ./configure --prefix=/$HOME/apps/xdrfile
> 
> This might not be the problem, but the HOME environment variable here 
> and below will normally start with a slash, and so you should not 
> preface it with another.
> 
> > make install
> >
> > everything seemed to go well and the make check said everything passed.
> >
> > So then I try a test code
> >
> >1 #include
> >2 #include "xdrfile_xtc.h"
> >3 using namespace std;
> >4
> >5 int main()
> >6 {
> >7
> >8  int natoms;
> >9  read_xtc_natoms("traj.xtc",&natoms);
> >   10 return 0;
> >   11 }
> >
> > and I compile with
> >
> > icc  -I/$HOME/apps/xdrfile/include/xdrfile  -L/$HOME/apps/xdrfile/lib/  
> > test.cpp
> >
> > and i get an error saying...
> >
> > undefined reference to 'read_xtc_natoms(char *, int*)'
> >
> > I am sure that I am doing something stupid. I tried a C compiler and 
> > linking to few other random places but, like I said, this stuff (installing 
> > libraries and linking) is new to me.
> > Please help.
> 
> icc  -I$HOME/apps/xdrfile/include/xdrfile test.cpp
> 
> will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h
> 
> Mark

-- 
Joshua L. Phillips
Ph.D. Candidate - School of Engineering
University of California, Merced
jphilli...@ucmerced.edu


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

[Tsjerk Wassenaar]

Hey Anirban,

I would consider the ions part of the solvent. But the procedure is right.

Cheers,

Tsjerk

On May 7, 2011 7:35 AM, "Anirban Ghosh" 
wrote:

Hi ALL,

I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms as calculation group and Protein as the output group. So I
need to make a group with Protein+Lipid+Ions as the calculation group.
Right?
Thanks a lot in advance.

Regards,

Anirban

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_sas query

[Anirban Ghosh]

Hello Tsjerk,

Thanks for the reply.
But if I consider the ions also in the calculation group, then it is not
wrong. Right?

Thanks,

Anirban

On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar  wrote:

> Hey Anirban,
>
> I would consider the ions part of the solvent. But the procedure is right.
>
> Cheers,
>
> Tsjerk
>
> On May 7, 2011 7:35 AM, "Anirban Ghosh" 
> wrote:
>
> Hi ALL,
>
> I want to calculate the SASA of a protein embedded in a bilayer along with
> water and ions. So while using g_sas I understand that I need to supply all
> non-solvent atoms as calculation group and Protein as the output group. So I
> need to make a group with Protein+Lipid+Ions as the calculation group.
> Right?
> Thanks a lot in advance.
>
> Regards,
>
> Anirban
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists