Re: [gmx-users] virtual sites

[Roland Schulz]

On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi  wrote:

> Dear Users,
>
> I have a system consisting of peptides and a linear carbohydrate.
> Initially I tried to simulate these peptides using virtual sites and
> it worked. I can use pdb2gmx for building virtual sites on protein
> whereas I have an itp file for the carbohydrate.

Yes you can modify the top file by hand to use itp files generated in two
different ways.


> Is it possible to
> apply virtual site to a carbohydrate along with the peptides?
>
If you have an rtp file for you carbohydrate you should be able to run
pdb2gmx and then you should also be able to generate vsite. Or you can
generate them using your own scripts. Of course you only need them if you
have the respective groups (e.g. CH3).

Roland


>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
> --
> 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
>
>
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-- 
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

[Justin Lemkul]

On 10/29/13 2:21 AM, Neha Gandhi wrote:

Dear Users,

I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
whereas I have an itp file for the carbohydrate. Is it possible to
apply virtual site to a carbohydrate along with the peptides?



Sure, have you tried?  Were there problems?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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] virtual sites

[Neha Gandhi]

Dear Users,

I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
whereas I have an itp file for the carbohydrate. Is it possible to
apply virtual site to a carbohydrate along with the peptides?

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
-- 
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 in gromacs

[Tsjerk Wassenaar]

Hi Neha,

Yes. The MN* particles are the virtual sites.

Cheers,

Tsjerk


On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi  wrote:

> Dear Users,
>
> I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am
> using following command.
>  pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh
>
> Upon visualisation I could see triangle like sites. Does the output seem
> right?
>
>75
> 1VALMN11   2.913   3.551   3.288
> 1VALMN22   2.880   3.575   3.356
> 1VAL  N3   2.891   3.561   3.320
> 1VAL H14   2.960   3.543   3.250
> 1VAL H25   2.887   3.659   3.339
> 1VAL H36   2.915   3.511   3.403
> 1VAL CA7   2.758   3.515   3.271
> 1VAL CB8   2.761   3.365   3.234
> 1VALCG19   2.628   3.322   3.174
> 1VALCG2   10   2.878   3.334   3.138
> 1VAL  C   11   2.651   3.542   3.379
> 1VAL  O   12   2.640   3.469   3.476
> 2GLN  N   13   2.578   3.652   3.361
> 2GLN  H   14   2.599   3.711   3.283
> 2GLN CA   15   2.467   3.691   3.449
> 2GLN CB   16   2.497   3.826   3.515
> 2GLN CG   17   2.399   3.863   3.627
> 2GLN CD   18   2.427   3.999   3.688
> 2GLNOE1   19   2.428   4.101   3.617
> 2GLNNE2   20   2.450   4.003   3.818
> 2GLN   HE21   21   2.449   3.918   3.872
> 2GLN   HE22   22   2.469   4.090   3.863
> 2GLN  C   23   2.342   3.700   3.363
> 2GLN  O   24   2.337   3.777   3.269
> 3ILE  N   25   2.242   3.620   3.396
> 3ILE  H   26   2.250   3.564   3.479
> 3ILE CA   27   2.119   3.610   3.317
> 3ILE CB   28   2.107   3.470   3.251
> 3ILECG1   29   2.228   3.440   3.162
> 3ILECG2   30   1.981   3.459   3.168
> 3ILE CD   31   2.257   3.295   3.151
> 3ILE  C   32   2.000   3.634   3.409
> 3ILE  O   33   1.985   3.563   3.508
> 4VAL  N   34   1.918   3.734   3.379
> 4VAL  H   35   1.936   3.789   3.297
> 4VAL CA   36   1.802   3.766   3.463
> 4VAL CB   37   1.817   3.903   3.533
> 4VALCG1   38   1.695   3.934   3.619
> 4VALCG2   39   1.944   3.903   3.618
> 4VAL  C   40   1.674   3.766   3.381
> 4VAL  O   41   1.664   3.838   3.283
> 5TYR  N   42   1.580   3.682   3.422
> 5TYR  H   43   1.602   3.617   3.494
> 5TYR CA   44   1.445   3.681   3.366
> 5TYR CB   45   1.400   3.537   3.337
> 5TYR CG   46   1.463   3.471   3.217
> 5TYRCD1   47   1.572   3.386   3.230
> 5TYRHD1   48   1.610   3.368   3.321
> 5TYRCD2   49   1.413   3.494   3.089
> 5TYRHD2   50   1.334   3.555   3.077
> 5TYRCE1   51   1.629   3.326   3.120
> 5TYRHE1   52   1.707   3.264   3.131
> 5TYRCE2   53   1.469   3.434   2.978
> 5TYRHE2   54   1.431   3.451   2.887
> 5TYR CZ   55   1.578   3.351   2.993
> 5TYR OH   56   1.632   3.291   2.882
> 5TYR HH   57   1.582   3.321   2.800
> 5TYR  C   58   1.352   3.741   3.471
> 5TYR  O   59   1.337   3.685   3.580
> 6LYS  N   60   1.290   3.853   3.439
> 6LYS  H   61   1.306   3.895   3.349
> 6LYS CA   62   1.197   3.917   3.532
> 6LYS CB   63   1.271   4.015   3.624
> 6LYS CG   64   1.323   4.142   3.559
> 6LYS CD   65   1.428   4.211   3.649
> 6LYS CE   66   1.468   4.349   3.597
> 6LYS   MNZ1   67   1.590   4.442   3.650
> 6LYS   MNZ2   68   1.594   4.377   3.696
> 6LYS NZ   69   1.587   4.407   3.670
> 6LYSHZ1   70   1.608   4.497   3.632
> 6LYSHZ2   71   1.565   4.416   3.767
> 6LYSHZ3   72   1.665   4.346   3.659
> 6LYS  C   73   1.080   3.982   3.461
> 6LYS O1   74   1.065   3.973   3.340
> 6LYS O2   75   0.988   4.044   3.539
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
> --
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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] virtual sites in gromacs

[Neha Gandhi]

Dear Users,

I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am
using following command.
 pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh

Upon visualisation I could see triangle like sites. Does the output seem right?

   75
1VALMN11   2.913   3.551   3.288
1VALMN22   2.880   3.575   3.356
1VAL  N3   2.891   3.561   3.320
1VAL H14   2.960   3.543   3.250
1VAL H25   2.887   3.659   3.339
1VAL H36   2.915   3.511   3.403
1VAL CA7   2.758   3.515   3.271
1VAL CB8   2.761   3.365   3.234
1VALCG19   2.628   3.322   3.174
1VALCG2   10   2.878   3.334   3.138
1VAL  C   11   2.651   3.542   3.379
1VAL  O   12   2.640   3.469   3.476
2GLN  N   13   2.578   3.652   3.361
2GLN  H   14   2.599   3.711   3.283
2GLN CA   15   2.467   3.691   3.449
2GLN CB   16   2.497   3.826   3.515
2GLN CG   17   2.399   3.863   3.627
2GLN CD   18   2.427   3.999   3.688
2GLNOE1   19   2.428   4.101   3.617
2GLNNE2   20   2.450   4.003   3.818
2GLN   HE21   21   2.449   3.918   3.872
2GLN   HE22   22   2.469   4.090   3.863
2GLN  C   23   2.342   3.700   3.363
2GLN  O   24   2.337   3.777   3.269
3ILE  N   25   2.242   3.620   3.396
3ILE  H   26   2.250   3.564   3.479
3ILE CA   27   2.119   3.610   3.317
3ILE CB   28   2.107   3.470   3.251
3ILECG1   29   2.228   3.440   3.162
3ILECG2   30   1.981   3.459   3.168
3ILE CD   31   2.257   3.295   3.151
3ILE  C   32   2.000   3.634   3.409
3ILE  O   33   1.985   3.563   3.508
4VAL  N   34   1.918   3.734   3.379
4VAL  H   35   1.936   3.789   3.297
4VAL CA   36   1.802   3.766   3.463
4VAL CB   37   1.817   3.903   3.533
4VALCG1   38   1.695   3.934   3.619
4VALCG2   39   1.944   3.903   3.618
4VAL  C   40   1.674   3.766   3.381
4VAL  O   41   1.664   3.838   3.283
5TYR  N   42   1.580   3.682   3.422
5TYR  H   43   1.602   3.617   3.494
5TYR CA   44   1.445   3.681   3.366
5TYR CB   45   1.400   3.537   3.337
5TYR CG   46   1.463   3.471   3.217
5TYRCD1   47   1.572   3.386   3.230
5TYRHD1   48   1.610   3.368   3.321
5TYRCD2   49   1.413   3.494   3.089
5TYRHD2   50   1.334   3.555   3.077
5TYRCE1   51   1.629   3.326   3.120
5TYRHE1   52   1.707   3.264   3.131
5TYRCE2   53   1.469   3.434   2.978
5TYRHE2   54   1.431   3.451   2.887
5TYR CZ   55   1.578   3.351   2.993
5TYR OH   56   1.632   3.291   2.882
5TYR HH   57   1.582   3.321   2.800
5TYR  C   58   1.352   3.741   3.471
5TYR  O   59   1.337   3.685   3.580
6LYS  N   60   1.290   3.853   3.439
6LYS  H   61   1.306   3.895   3.349
6LYS CA   62   1.197   3.917   3.532
6LYS CB   63   1.271   4.015   3.624
6LYS CG   64   1.323   4.142   3.559
6LYS CD   65   1.428   4.211   3.649
6LYS CE   66   1.468   4.349   3.597
6LYS   MNZ1   67   1.590   4.442   3.650
6LYS   MNZ2   68   1.594   4.377   3.696
6LYS NZ   69   1.587   4.407   3.670
6LYSHZ1   70   1.608   4.497   3.632
6LYSHZ2   71   1.565   4.416   3.767
6LYSHZ3   72   1.665   4.346   3.659
6LYS  C   73   1.080   3.982   3.461
6LYS O1   74   1.065   3.973   3.340
6LYS O2   75   0.988   4.044   3.539

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
-- 
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 parameters

[Justin Lemkul]

On 6/18/13 12:20 PM, Bastien Loubet wrote:

Dear GROMACS user,

I have been trying to define parameters for virtual sites in CHARMM lipid,
and I would like to know if there is something simillar to the [ bondtypes ]
for virtual sites.
Specifically the way I specify the parameters now is by having lines in the
topology such as (for a 3fout virtual sites):

[ virtual_sites3 ]
;  aiajakal functc0c1c2
40393751 4 -0.26909  -0.26909  4.5519

But then I have to do that for every virtual sites in the molecule, even if
the parameters are the same.
What I would like to be able to do is:
[  ]
;  aiajakal functc0c1c2
H C CC 4 -0.26909  -0.26909  4.5519

and then
[ virtual_sites3 ]
;  aiajakal functc0c1c2
40393751 4

Where atom 40 is of type H and atom 39, 37 and 51 of type C and  should
be are directive similar to [ bondtypes ] but for virtual site.
Does this  directive exist ? I had no luck checking the manual.



Not likely, because virtual sites aren't generally built based on types, but 
based on specific atoms.  The workaround that came to mind is to make use of 
#define macros, like how the Gromos96 force fields define bonded terms.  You can 
simply:


#define param -0.26909 -0.26909 4.5519

Then, for your virtual sites:

[ virtual_sites3 ]
;  aiajakal functc0c1c2
   40393751 4   param

Not quite as efficient as defining types, but since that's not an option, it 
does save some typing.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Virtual sites parameters

[Bastien Loubet]

Dear GROMACS user,

I have been trying to define parameters for virtual sites in CHARMM lipid,
and I would like to know if there is something simillar to the [ bondtypes ]
for virtual sites.
Specifically the way I specify the parameters now is by having lines in the
topology such as (for a 3fout virtual sites):

[ virtual_sites3 ]
;  aiajakal functc0c1c2
   40393751 4 -0.26909  -0.26909  4.5519

But then I have to do that for every virtual sites in the molecule, even if
the parameters are the same.
What I would like to be able to do is:
[  ]
;  aiajakal functc0c1c2
   H C CC 4 -0.26909  -0.26909  4.5519

and then
[ virtual_sites3 ]
;  aiajakal functc0c1c2
   40393751 4 

Where atom 40 is of type H and atom 39, 37 and 51 of type C and  should
be are directive similar to [ bondtypes ] but for virtual site.
Does this  directive exist ? I had no luck checking the manual.

Best regards,

Bastien Loubet




--
View this message in context: 
http://gromacs.5086.x6.nabble.com/Virtual-sites-parameters-tp5009258.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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 setting

[Broadbent, Richard]

Dear Rajiv,

Without a clear explanation of what you are doing and the specific error
message from grompp it is impossible to offer any sensible advice.

Other pieces of information which might be useful would be, the topology
file, the actual grompp line, and the gro file for a single CO molecule

Richard

On 28/03/2013 20:02, "라지브간디"  wrote:

>Dear gmx,
>
>I would like to set virtual sites for CO molecules with some specific
>charge. 
>
>As per GROMACS manual, I've created virtual site2 in topology file for
>CO. Also, given the information in .rtp file as well as added the
>COM(center of mass) atom in .gro file. However, when I use gromp, it
>shows COM not found.
>
>Please need an advice. Thanks.
>
>Rajiv

-- 
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] Virtual sites setting

[라지브간디]

Dear gmx,

I would like to set virtual sites for CO molecules with some specific charge. 

As per GROMACS manual, I've created virtual site2 in topology file for CO. 
Also, given the information in .rtp file as well as added the COM(center of 
mass) atom in .gro file. However, when I use gromp, it shows COM not found. 

Please need an advice. Thanks. 

Rajiv-- 
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 in reference structure

[Tsjerk Wassenaar]

Hi Ahmet,

What is an incorrect RMSD? What is a correct RMSD? If you want to
calculate a backbone RMSD and you include side chain atoms, that's
wrong. Likewise, if you want to calculate a heavy atom, or
protein-all-atom RMSD and include virtual sites, that's wrong. If you
want to calculate an all-particle RMSD and you include virtual sites,
that's correct. If you do a mass-weighted RMSD, the contributions of
(those) virtual sites are always zero, because they don't have mass.
For the SASA, it's a bit of a different story. The area of a virtual
site should be zero, but I'm not sure if that's handled correctly. If
the virtual site is identified as unknown atom, then it is assigned a
default radius, which will give wrong results. But it's easy to
circumvent by choosing proper index groups.

Hope it helps,

Tsjerk

On Thu, Feb 21, 2013 at 9:33 AM, Ahmet yıldırım  wrote:
> Dear Tsjerk,
>
> Do the virtual sites cause incorrect calculations of SASA, RMSD or something
> else?
>
> Regards
> 2013/2/21 Tsjerk Wassenaar 
>
>> Hi Ahmet,
>>
>> You can always use suitable index groups for analysis.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım 
>> wrote:
>> > I thought the virtual sites can affect analysis.For example, dont they
>> cause
>> > incorrect calculations of SASA, RMSD or something else?
>> >
>> > Thanks in advance
>> >
>> > 2013/2/20 Justin Lemkul 
>> >
>> >>
>> >>
>> >> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
>> >>
>> >>> Dear users,
>> >>>
>> >>> I have the virtual sites in reference structure and all trajectory.
>> When
>> >>> analyzing simulation, do I have to get rid of those(virtual sites)? If
>> >>> yes/no, why?
>> >>>
>> >>>
>> >> Why do you think you need to remove them?
>> >>
>> >> -Justin
>> >>
>> >> --
>> >> ==**==
>> >>
>> >> Justin A. Lemkul, Ph.D.
>> >> Research Scientist
>> >> Department of Biochemistry
>> >> Virginia Tech
>> >> Blacksburg, VA
>> >> jalemkul[at]vt.edu | (540) 231-9080
>> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>
>> >> ==**==
>> >> --
>> >> gmx-users mailing listgmx-users@gromacs.org
>> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >> * Please search the archive at http://www.gromacs.org/**
>> >> Support/Mailing_Lists/Search<
>> 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<
>> http://www.gromacs.org/Support/Mailing_Lists>
>> >>
>> >
>> >
>> >
>> > --
>> > Ahmet Yıldırım
>> > --
>> > 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
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Biocomputing Group
>> Department of Biological Sciences
>> 2500 University Drive NW
>> Calgary, AB T2N 1N4
>> Canada
>> --
>> 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
>>
>
>
>
> --
> Ahmet Yıldırım
> --
> 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



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
--
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 in reference structure

[Ahmet yıldırım]

Dear Tsjerk,

Do the virtual sites cause incorrect calculations of SASA, RMSD or something
else?

Regards
2013/2/21 Tsjerk Wassenaar 

> Hi Ahmet,
>
> You can always use suitable index groups for analysis.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım 
> wrote:
> > I thought the virtual sites can affect analysis.For example, dont they
> cause
> > incorrect calculations of SASA, RMSD or something else?
> >
> > Thanks in advance
> >
> > 2013/2/20 Justin Lemkul 
> >
> >>
> >>
> >> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
> >>
> >>> Dear users,
> >>>
> >>> I have the virtual sites in reference structure and all trajectory.
> When
> >>> analyzing simulation, do I have to get rid of those(virtual sites)? If
> >>> yes/no, why?
> >>>
> >>>
> >> Why do you think you need to remove them?
> >>
> >> -Justin
> >>
> >> --
> >> ==**==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>
> >> ==**==
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
> 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<
> http://www.gromacs.org/Support/Mailing_Lists>
> >>
> >
> >
> >
> > --
> > Ahmet Yıldırım
> > --
> > 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
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
> --
> 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
>



-- 
Ahmet Yıldırım
--
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 in reference structure

[Tsjerk Wassenaar]

Hi Ahmet,

You can always use suitable index groups for analysis.

Cheers,

Tsjerk

On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım  wrote:
> I thought the virtual sites can affect analysis.For example, dont they cause
> incorrect calculations of SASA, RMSD or something else?
>
> Thanks in advance
>
> 2013/2/20 Justin Lemkul 
>
>>
>>
>> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
>>
>>> Dear users,
>>>
>>> I have the virtual sites in reference structure and all trajectory. When
>>> analyzing simulation, do I have to get rid of those(virtual sites)? If
>>> yes/no, why?
>>>
>>>
>> Why do you think you need to remove them?
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet Yıldırım
> --
> 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



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
--
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 in reference structure

[Ahmet yıldırım]

I thought the virtual sites can affect analysis.For example, dont they cause
incorrect calculations of SASA, RMSD or something else?

Thanks in advance

2013/2/20 Justin Lemkul 

>
>
> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I have the virtual sites in reference structure and all trajectory. When
>> analyzing simulation, do I have to get rid of those(virtual sites)? If
>> yes/no, why?
>>
>>
> Why do you think you need to remove them?
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Ahmet Yıldırım
--
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 in reference structure

[Justin Lemkul]

On 2/20/13 9:18 AM, Ahmet yıldırım wrote:

Dear users,

I have the virtual sites in reference structure and all trajectory. When
analyzing simulation, do I have to get rid of those(virtual sites)? If
yes/no, why?



Why do you think you need to remove them?

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] virtual sites in reference structure

[Ahmet yıldırım]

Dear users,

I have the virtual sites in reference structure and all trajectory. When
analyzing simulation, do I have to get rid of those(virtual sites)? If
yes/no, why?

Regards
-- 
Ahmet Yıldırım
--
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] Virtual sites LJ/mass

[dakoenig]

Dear Gromacs-Experts,

for my simulations of pure hexane (united atom model) I would like to
separate the mass and the interaction parameters of the CH3. So far I tried
several different setups by using virtual sites but none of them is working.
I hope somebody can help.

Here is some background information:

My "normal" hexane molecule looks like that:
CH3-CH2-CH2-CH2-CH2-CH3

The molecule with the separated mass and interaction parameters (LJ) should
look like that:
LJ[CH3]-Mass[CH3]-CH2-CH2-CH2-CH2-Mass[CH3]-LJ[CH3]

Is a setup like that possible?

Here is my topology file:

[ atomtypes ]
;nameat.nummass charge   ptype   VW
CH3615.0350  0A 0  
0
VSI 60   0V   
CH2614.0270  0A 

[ moleculetype ]
; Namenrexcl
Hexane  4

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1   VSI 1  HEX VSI 10.00
 2   CH3 1  HEX CH3 10.015.0350   
 3   CH2 1  HEX CH2 20.014.0270   
 4   CH2 1  HEX CH2 20.014.0270   
 5   CH2 1  HEX CH2 30.014.0270   
 6   CH2 1  HEX CH2 30.014.0270   
 7   CH3 1  HEX CH3 40.015.0350
 8   VSI 1  HEX VSI 40.00 

[ bonds ]
; ai  aj  fub_0 k_b
   2   1   20.0066  71500
   3   2   20.153   71500
   4   3   20.153   71500
   5   4   20.153   71500
   6   5   20.153   71500
   7   6   20.153   71500
   8   7   20.0066  71500

[ virtual_sites3 ]
; Site  from  futhetad
  1 4  3  2   3 180  0.0066
  8 5  6  7   3 180  0.0066

[ pairs ]
;ai  aj  fu
  1   6   1
  3   8   1

[ constraints ]
;  ai  aj  fu   b
   2   3   10.153
   3   4   10.153
   4   5   10.153
   5   6   10.153
   6   7   10.153
   
[ angles ]
; ai  aj  ak  futheta k_theta
   1   2   3   2180   52000
   2   3   4   2
   3   4   5   2
   4   5   6   2   
   5   6   7   2
   6   7   8   2180   52000

[ dihedrals ]
; ai  aj  ak  al  fu  C_1 C_2   C_3   C_4
   5   4   3   1   5  
   6   5   4   3   5  
   8   6   5   4   5

By executing an energy minimization the hexane molecules are folding
themselves together. Since all simulations with "normal" hexane molecules
are working fine, I guess there is no problem with the .gro or .mdp file.

Any help is highly appreciated. Thank you very much!

Merry X-Mas and happy new year :)

Daniel  




--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Virtual-sites-LJ-mass-tp5003990.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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] virtual sites with CHARMM lipids

[Bastien Loubet]

Dear GROMACS users,

I have been working on a CHARMM36 POPC bilayer and in order to accelerate
the simulation we want to use virtual sites for the hydrogen atoms in the
lipid.

We mainly want to do it for the carbon tails of the lipids.
I have checked the different type of virtual sites in the GROMACS manual
(3fd, 3fda, 3out, N) but none of them seems to correspond to the CH2 groups
in the carbon chains.
It would require an out of plane virtual site with fixed length (so using
normalized vector).

Can you help me with that ?

Thanks,

Bastien Loubet



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/virtual-sites-with-CHARMM-lipids-tp5003962.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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 - remove from GRO

[Steven Neumann]

On Mon, May 14, 2012 at 1:51 PM, Mark Abraham wrote:

> On 14/05/2012 10:42 PM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> i run the implicit simulation with virtual sites on the hydrogen of my
>> protein. Now I want to extract coordinates and run another simulation (in
>> explicit solvent). Is there any way to remove those virtual sites from my
>> gro file as VMD write the file using atoms not recognized by pdb2gmx
>> obviously? Please, help!
>>
>
> If your original pdb2gmx workflow with virtual sites was recorded in a
> shell script you'd
> a) have a record for when you go to write up, and
> b) be able to do this change easily.
>
> As it is, a few minutes with a text editor would probably work for small
> systems. Alternatively
>
> grep -v MCH3 in.gro > temp.gro
>
> will remove all of the lines for virtual sites named MCH3. Do that for
> each type of virtual site. Adjust the count of atoms at the top of the .gro
> file suitably at the end.
>
> Mark


Thank you Mark!

Steven

>
> --
> 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/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**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 - remove from GRO

[Mark Abraham]

On 14/05/2012 10:42 PM, Steven Neumann wrote:

Dear Gmx Users,

i run the implicit simulation with virtual sites on the hydrogen of my 
protein. Now I want to extract coordinates and run another simulation 
(in explicit solvent). Is there any way to remove those virtual sites 
from my gro file as VMD write the file using atoms not recognized by 
pdb2gmx obviously? Please, help!


If your original pdb2gmx workflow with virtual sites was recorded in a 
shell script you'd

a) have a record for when you go to write up, and
b) be able to do this change easily.

As it is, a few minutes with a text editor would probably work for small 
systems. Alternatively


grep -v MCH3 in.gro > temp.gro

will remove all of the lines for virtual sites named MCH3. Do that for 
each type of virtual site. Adjust the count of atoms at the top of the 
.gro file suitably at the end.


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

Re: [gmx-users] Virtual Sites - remove from GRO

[Justin A. Lemkul]

On 5/14/12 8:42 AM, Steven Neumann wrote:

Dear Gmx Users,

i run the implicit simulation with virtual sites on the hydrogen of my protein.
Now I want to extract coordinates and run another simulation (in explicit
solvent). Is there any way to remove those virtual sites from my gro file as VMD
write the file using atoms not recognized by pdb2gmx obviously? Please, help!



Virtual sites have rather obvious names that lend themselves well to being 
grepped out, i.e.:


grep -v "M[CN]" conf.gro > conf_clean.gro

Adjust the number of atoms in conf_clean.gro and proceed.

-Justin

--


Justin A. Lemkul, Ph.D.
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] Virtual Sites - remove from GRO

[Steven Neumann]

Dear Gmx Users,

i run the implicit simulation with virtual sites on the hydrogen of my
protein. Now I want to extract coordinates and run another simulation (in
explicit solvent). Is there any way to remove those virtual sites from my
gro file as VMD write the file using atoms not recognized by pdb2gmx
obviously? Please, help!

Steven
-- 
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 in a polymer backbone

[Broadbent, Richard]

> 
> Any particular reason why improper dihedrals would not be suitable?  They are
> significantly easier to implement.
Yes the force field parameters for the molecule are not known and I am
therefore fitting the parameters to Density Functional Theory. If I allow
the units to move out of plane even slightly their will be additional
parameters to fit which will make the problem unfeasibly computationally
expensive.

Thank you for the suggestion,

Richard

--
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 in a polymer backbone

[Justin A. Lemkul]

Broadbent, Richard wrote:

I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the
polymer. 


I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as phenyl rings and
connected 5 and 6 member rings (similar to Phthalimide) with 3 reference
sites, then virtualise all the atomic sites. I'm going to use standard type
3 virtual sites and planned on constraining the relative positions of the 3
reference points. 


My plan is to pick sites such that the 3 eigenvalues of the moment of
inertia tensor, the centre of mass, and the total mass of the system are
conserved. As the system is two dimensional this amounts to a total of 6
non-linear equations for 9 variables which requires either additional
constraints or a physically motivated guess to solve.

I've searched the mailing list but have been unable to find any previous
attempts at this. I was wondering if anyone knew of a reference where this
had been attempted or if there had been any previous discussions about an
approach similar to this?

I am also very open to alternative approaches to holding these groups
planar.



Any particular reason why improper dihedrals would not be suitable?  They are 
significantly easier to implement.


-Justin


Many thanks,

Richard



--


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] Virtual Sites in a polymer backbone

[Broadbent, Richard]

I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the
polymer. 

I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as phenyl rings and
connected 5 and 6 member rings (similar to Phthalimide) with 3 reference
sites, then virtualise all the atomic sites. I'm going to use standard type
3 virtual sites and planned on constraining the relative positions of the 3
reference points. 

My plan is to pick sites such that the 3 eigenvalues of the moment of
inertia tensor, the centre of mass, and the total mass of the system are
conserved. As the system is two dimensional this amounts to a total of 6
non-linear equations for 9 variables which requires either additional
constraints or a physically motivated guess to solve.

I've searched the mailing list but have been unable to find any previous
attempts at this. I was wondering if anyone knew of a reference where this
had been attempted or if there had been any previous discussions about an
approach similar to this?

I am also very open to alternative approaches to holding these groups
planar.

Many thanks,

Richard

--
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

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

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]

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] 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

[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

[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

[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 10:17 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]

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

[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]

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:

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]

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:

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]

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
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
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

[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

[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

[Sikandar Mashayak]

 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 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 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

[Sikandar Mashayak]

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  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

[Gavin Melaugh]

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

Re: [gmx-users] virtual sites

[Justin A. Lemkul]

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

--


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

[Gavin Melaugh]

Hi Sikandar

Many Thanks for the reply. When you define energygrps in the mdp file,
does that mean that only these groups are written to the energy file. I
take it that all iother information regarding the energy is written as
well i.e if you left this section blank

Cheers

Gavin

Sikandar Mashayak wrote:
> you can do it as following
>
> 1. create index file make_indx -f conf.gro -n index.ndx ( select VS
> and any other atoms you want lets say OTHERS)
> 2. in .mdp define energygrps "VS OTHERS"
> 3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp
> file
>
> for more you can refer to manual..
>
> I hope it helps
>
> --
> sikandar
>
>
>
> On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh  > wrote:
>
> Hi Sikandar
>
> Cheers. How do you actually define the energy groups?
>
> Gavin
>
> Sikandar Mashayak wrote:
> > yes, you can make virtual sites interact with only specific sites by
> > using Energy Exclusion between energy groups. This can be done by
> > defining energy groups for virtual sites and other atoms, then
> exclude
> > or include the non-bonded interactions between them accordingly...
> >
> > On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh
> mailto:gmelaug...@qub.ac.uk>
> > >> wrote:
> >
> > Hi All
> >
> > Is it possible to have a virtual site interact with only
> specific
> > atoms
> > and not interact at all with everything else?
> >
> >
> > Cheers
> >
> > Gavin
> > --
> > 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

Re: [gmx-users] virtual sites

[Gavin Melaugh]

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 .

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Sikandar
>>
>> Cheers. How do you actually define the energy groups?
>>
>
> Read in the manual about the .mdp option "energygrps" and apply custom
> index groups as necessary.
>
> -Justin
>
>> Gavin
>>
>> Sikandar Mashayak wrote:
>>> yes, you can make virtual sites interact with only specific sites by
>>> using Energy Exclusion between energy groups. This can be done by
>>> defining energy groups for virtual sites and other atoms, then exclude
>>> or include the non-bonded interactions between them accordingly...
>>>
>>> On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh >> > wrote:
>>>
>>> Hi All
>>>
>>> Is it possible to have a virtual site interact with only specific
>>> atoms
>>> and not interact at all with everything else?
>>>
>>>
>>> Cheers
>>>
>>> Gavin
>>> --
>>> 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

[Sikandar Mashayak]

you can do it as following

1. create index file make_indx -f conf.gro -n index.ndx ( select VS and any
other atoms you want lets say OTHERS)
2. in .mdp define energygrps "VS OTHERS"
3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp file

for more you can refer to manual..

I hope it helps

--
sikandar



On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh  wrote:

> Hi Sikandar
>
> Cheers. How do you actually define the energy groups?
>
> Gavin
>
> Sikandar Mashayak wrote:
> > yes, you can make virtual sites interact with only specific sites by
> > using Energy Exclusion between energy groups. This can be done by
> > defining energy groups for virtual sites and other atoms, then exclude
> > or include the non-bonded interactions between them accordingly...
> >
> > On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh  > > wrote:
> >
> > Hi All
> >
> > Is it possible to have a virtual site interact with only specific
> > atoms
> > and not interact at all with everything else?
> >
> >
> > Cheers
> >
> > Gavin
> > --
> > 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

Re: [gmx-users] virtual sites

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Sikandar

Cheers. How do you actually define the energy groups?



Read in the manual about the .mdp option "energygrps" and apply custom index 
groups as necessary.


-Justin


Gavin

Sikandar Mashayak wrote:

yes, you can make virtual sites interact with only specific sites by
using Energy Exclusion between energy groups. This can be done by
defining energy groups for virtual sites and other atoms, then exclude
or include the non-bonded interactions between them accordingly...

On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh mailto:gmelaug...@qub.ac.uk>> wrote:

Hi All

Is it possible to have a virtual site interact with only specific
atoms
and not interact at all with everything else?


Cheers

Gavin
--
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

[Gavin Melaugh]

Hi Sikandar

Cheers. How do you actually define the energy groups?

Gavin

Sikandar Mashayak wrote:
> yes, you can make virtual sites interact with only specific sites by
> using Energy Exclusion between energy groups. This can be done by
> defining energy groups for virtual sites and other atoms, then exclude
> or include the non-bonded interactions between them accordingly...
>
> On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh  > wrote:
>
> Hi All
>
> Is it possible to have a virtual site interact with only specific
> atoms
> and not interact at all with everything else?
>
>
> Cheers
>
> Gavin
> --
> 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

[Sikandar Mashayak]

yes, you can make virtual sites interact with only specific sites by using
Energy Exclusion between energy groups. This can be done by defining energy
groups for virtual sites and other atoms, then exclude or include the
non-bonded interactions between them accordingly...

On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh  wrote:

> Hi All
>
> Is it possible to have a virtual site interact with only specific atoms
> and not interact at all with everything else?
>
>
> Cheers
>
> Gavin
> --
> 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] virtual sites

[Gavin Melaugh]

Hi All

Is it possible to have a virtual site interact with only specific atoms
and not interact at all with everything else?


Cheers

Gavin
-- 
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 and heavy atoms for longer time steps

[Mark Abraham]

On 2/12/2010 11:13 AM, Hassan Shallal wrote:

I have some issues to discuss with the mailing list users,

1- Is using virtual sites alone enough to allow me to lengthen the time step 
from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology 
files in order to use 4 fs time step?

2- Another question, does vitual sites (assigning virtual hydrogens a mass of 
zero and adding their masses to the connected heavy atoms) opposes the effect 
of heavy atoms (increases the mass of the hydroen atoms) or vice versa.
Or is the situation that heavy atoms treatment applies  when virtual sites 
treatment is not implemented, and we end up with a systme where some hydrogen 
atoms have no masses at all (those as virtual sites) whereas other hydrogen 
atoms are much heavier (those treated as heavy hydrogens)?

3- Implementing the scenario of some hydrogen atoms having zero masses and 
others having heavier masses, how would that affect the accuracy of predicting 
some energetic aspects like H-bonding? I know there is always a trade between 
efficiency or fastness and the accuracy because approximations usually fasten 
the job while decreasing the accuracy, but from experienced users point of 
view, how dangerous that approximation would be?

Any answers or clarification of the above issues will be so much appreciated


Perhaps manual section 6.5 and ref therein will clarify some of this.

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] virtual sites and heavy atoms for longer time steps

[Hassan Shallal]

I have some issues to discuss with the mailing list users,
 
1- Is using virtual sites alone enough to allow me to lengthen the time step 
from 2 fs to 4 fs, or I have also to use heavy hydrogens when creating topology 
files in order to use 4 fs time step?
 
2- Another question, does vitual sites (assigning virtual hydrogens a mass of 
zero and adding their masses to the connected heavy atoms) opposes the effect 
of heavy atoms (increases the mass of the hydroen atoms) or vice versa. 
Or is the situation that heavy atoms treatment applies  when virtual sites 
treatment is not implemented, and we end up with a systme where some hydrogen 
atoms have no masses at all (those as virtual sites) whereas other hydrogen 
atoms are much heavier (those treated as heavy hydrogens)?
 
3- Implementing the scenario of some hydrogen atoms having zero masses and 
others having heavier masses, how would that affect the accuracy of predicting 
some energetic aspects like H-bonding? I know there is always a trade between 
efficiency or fastness and the accuracy because approximations usually fasten 
the job while decreasing the accuracy, but from experienced users point of 
view, how dangerous that approximation would be?
 
Any answers or clarification of the above issues will be so much appreciated
 
Hassan



From: gmx-users-boun...@gromacs.org on behalf of Roland Schulz
Sent: Wed 12/1/2010 2:15 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Cut-offs using CHARMM27 ff




On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal  wrote:


Dear Gromacs users,
 
I am trying to use CHARMM27 taking the simulation conditions of two 
recent articles as guides in optimizing the simulation parameters. (DOI: 
10.1021/ct900549r and DOI: 10.1021/jp101581h). 
 
-- Both are using PME for electrostatics and I am planning to do that 
too
-- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force 
field as mentioned)
-- In the second paper, they have explicitly assigned rvdw = 1.2 (this 
value is also optimized for CHARMM27 force field) and they assigned the NS 
rlist = 1.2 because as I understand, using PME as a coulombtype requires 
rcoulomb to be equal to rlist. I have no problem following up until now and it 
seems that (rlist = rcoulomb = rvdw = 1.2) presents the best combination of 
cut-offs for using (coulombtype = PME and vdwtype = cut-off) along with CHARMM27
 
-- What I can't get is that in the first paper, they mentioned the 
following "van der Waals interactions were switched off between 1.0 to 1.2 nm"
what does that mean in terms of cut-offs and vdwtype?
Does that mean vdwtype = switch, vdw_switch = 1, rvdw = 1.2 ? 

yes. 


and if this is what is meant, then rlist has to be 0.1-0.3 larger than 
rvdw to accomodate for the size of the charge groups as mentioned in the manual 
and accordingly, we can't keep rcoulomb = 1.2 because rcoulomb must be equal to 
rlist to allow using PME.

CHARMM FF doesn't use charge groups. Thus (as far as I understand) this warning 
can be ignored.  You still miss a few interactions because the neighbor-list 
only contains everything up to 1.2 thus an atom at a distance just above 1.2 
and moves a bit inwards, it is not included until the next neighbor-list 
update. But because the interaction is already switched it is not very critical 
in my opinion. If you want to avoid this you can use PME-Switch but this is 
significant slower.

Roland 


 
 
 

--
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





-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov  
865-241-1537, ORNL PO BOX 2008 MS6309

<>-- 
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

[Mark Abraham]

zhang wrote:

Dear users,
 I use the Cationic Dummy Atom methods by Pang to simulate a protein 
containing Zn2+. How to get the parameters in [ virtual_sites? ] 
section? I use the model  4fd.
 In the following example, how to get the value of parameters a, b 
and d?


   [ virtual sites4 ]

   ; Site from funct a b d

   5 1 2 3 4 1 0.3 0.3 -0.105

 Thanks in advance!


Have you read the manual section on virtual sites, and consulted the 
part of manual chapter 5 to see how this part might work?


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

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] virtual sites

[zhang]

Dear users,
 I use the Cationic Dummy Atom methods by Pang to simulate a protein 
containing Zn2+. How to get the parameters in [ virtual_sites? ] section? I use 
the model  4fd.
 In the following example, how to get the value of parameters a, b and d? 

   [ virtual sites4 ]

   ; Site from funct a b d

   5 1 2 3 4 1 0.3 0.3 -0.105

 Thanks in advance!

 

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