[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[Alan]

Thanks dear Chris and Berk.

Indeed I contact Eric but still waiting a reply. BTW, the whole point I am
trying here is to try to reproduce his results and apply to validate my
application ACPYPE, which uses ANTECHAMBER.

Thanks Berk for explaining about the Kinetic energy.

And Chris:

On Tue, Jul 27, 2010 at 15:57,  wrote:

> Dear Alan:
>
> (although you should try gromacs compiled in double precision).
>

I did, same results.


>  I can reproduce the non-zero kinetic energy with a single spc water,
> as long as I add define=-DFLEXIBLE to the .mdp file. The output .gro
> contains all zeroes for velocities (as long as the input .gro does not
> contain any velocities!):
>

I was hoping that my error would be something simple like forgetting
"define=-DFLEXIBLE", but adding that made no difference yet.


> I added unconstrainted_start=yes to your .mdp file but that did not help.
>

I am using GMX 4.0.5 and if I add "unconstrainted_start=yes" I got a error:

WARNING 1 [file SPE.mdp, line unknown]:
  Unknown or double left-hand 'unconstrainted_start' in parameter file

I never heard about this option.

I tried the same system in CNS/XPLOR and the results matched AMBER and NAMD.
So far only GROMACS looks awkward.

Thanks,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[Alan]

Thanks Ilja,

On Tue, Jul 27, 2010 at 16:36,  wrote:

> I think the bond terms differ simply due to the round off error. The gro
> file is worse than pdb when it comes to round off in Cartesian coordinates.
> You can confirm this is the case by taking your gro file and converting it
> back to pdb using gromacs tools and then use the resulting pdb (with the
> same round of as the gro file now) file from gromacs in NAMD. You should
> see
> the same numbers for bonded terms then.
>

I doubt that would do any difference.

Anyway, I tested with double precision and found out that my gro file is
still rounded off like in single precision, i.e., my gro in double is the
same in single and I was not expecting that.

Example:

pdb: 13  N   ALA A   2   1.927   1.789   1.165  1.00  0.00

gro (single or double): 2ALA  N   13   0.193   0.179   0.117


I was expecting gro when using pdb2gmx_d to be like:

gro (single or double): 2ALA  N   13   0.192700   0.178900   0.165000

Hummm I don't like this.


Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[chris . neale]

Alan: you should try Ilja's suggestion, it was a good one. The idea is  
that during pdb2gmx you may have obtained a .gro file that was rounded  
and then you may have used this .gro as input to grompp and so your  
run did not start with the exact same coordinates in gromacs and namd.  
A similar test would be to be sure that you run grompp with the same  
.pdb file that you used in namd, etc. (or perhaps you already did that?)


Actually, from what you post below I think that you have your answer.  
Use the orig .pdb into grompp and things should be ok, probably even  
in single precision, although the output .gro will be rounded as you  
see.


PS: let's keep a positive mood.

Chris.

On Tue, Jul 27, 2010 at 16:36,  wrote:


I think the bond terms differ simply due to the round off error. The gro
file is worse than pdb when it comes to round off in Cartesian coordinates.
You can confirm this is the case by taking your gro file and converting it
back to pdb using gromacs tools and then use the resulting pdb (with the
same round of as the gro file now) file from gromacs in NAMD. You should
see
the same numbers for bonded terms then.



I doubt that would do any difference.

Anyway, I tested with double precision and found out that my gro file is
still rounded off like in single precision, i.e., my gro in double is the
same in single and I was not expecting that.

Example:

pdb: 13  N   ALA A   2   1.927   1.789   1.165  1.00  0.00

gro (single or double): 2ALA  N   13   0.193   0.179   0.117


I was expecting gro when using pdb2gmx_d to be like:

gro (single or double): 2ALA  N   13   0.192700   0.178900   0.165000

Hummm I don't like this.


Alan
--


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

[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[Alan]

First of all, thanks a lot guys, in special Ilja and Chris.

Indeed, Ilja's observation proved to be corrected, and as Chris suggested,
using the pdb instead of the gro for grompp and the energies matched.

However, I am still uneasy with the fact that pdb2gmx_d and mdrun_d is not
generating a gro with at least 6 decimals instead of the usual 3.

Many thanks,

Alan

On Tue, Jul 27, 2010 at 20:34,  wrote:

> Alan: you should try Ilja's suggestion, it was a good one. The idea is
> that during pdb2gmx you may have obtained a .gro file that was rounded
> and then you may have used this .gro as input to grompp and so your
> run did not start with the exact same coordinates in gromacs and namd.
> A similar test would be to be sure that you run grompp with the same
> .pdb file that you used in namd, etc. (or perhaps you already did that?)
>
> Actually, from what you post below I think that you have your answer.
> Use the orig .pdb into grompp and things should be ok, probably even
> in single precision, although the output .gro will be rounded as you
> see.
>
> PS: let's keep a positive mood.
>
> Chris.
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[Justin A. Lemkul]

Alan wrote:

Thanks dear Chris and Berk.

Indeed I contact Eric but still waiting a reply. BTW, the whole point I 
am trying here is to try to reproduce his results and apply to validate 
my application ACPYPE, which uses ANTECHAMBER.


Thanks Berk for explaining about the Kinetic energy.

And Chris:

On Tue, Jul 27, 2010 at 15:57, > wrote:


Dear Alan:

(although you should try gromacs compiled in double precision).


I did, same results.
 


I can reproduce the non-zero kinetic energy with a single spc water,
as long as I add define=-DFLEXIBLE to the .mdp file. The output .gro
contains all zeroes for velocities (as long as the input .gro does not
contain any velocities!):


I was hoping that my error would be something simple like forgetting 
"define=-DFLEXIBLE", but adding that made no difference yet.
 


I added unconstrainted_start=yes to your .mdp file but that did not
help.


I am using GMX 4.0.5 and if I add "unconstrainted_start=yes" I got a error:

WARNING 1 [file SPE.mdp, line unknown]:
  Unknown or double left-hand 'unconstrainted_start' in parameter file

I never heard about this option.
 


Typo: the option "unconstrained_start" should be replaced by "continuation" in 
the 4.0.x series; grompp will replace it for you if the old option is present.


-Justin

I tried the same system in CNS/XPLOR and the results matched AMBER and 
NAMD. So far only GROMACS looks awkward.


Thanks,

Alan

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
 >>http://www.bio.cam.ac.uk/~awd28<<



--


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


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

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

RE: [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

[Berk Hess]

Hi,

The gro file format, just like the pdb format, is an ancient fixed format.
Thus it supports only 3 decimals.
Note that this has nothing to do with single or double precision (which have a 
range
of rougly 10^7 and 10^16).

If pdb2gmx does not mess with your hydrogen and terminal atom coordinates
(as some old versions did), you can use pdb2gmx -o conf.pdb for pdb coordinate 
output
or -o conf.g96 for lots of decimals. All Gromacs programs can read pdb and g96
instead of gro files.

Berk

From: alanwil...@gmail.com
Date: Wed, 28 Jul 2010 07:45:50 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: gromacs energies very different from other MD  engine 
for the very same system and condition

First of all, thanks a lot guys, in special Ilja and Chris.
Indeed, Ilja's observation proved to be corrected, and as Chris suggested, 
using the pdb instead of the gro for grompp and the energies matched.


However, I am still uneasy with the fact that pdb2gmx_d and mdrun_d is not 
generating a gro with at least 6 decimals instead of the usual 3.
Many thanks,


Alan

On Tue, Jul 27, 2010 at 20:34,   wrote:


Alan: you should try Ilja's suggestion, it was a good one. The idea is

that during pdb2gmx you may have obtained a .gro file that was rounded

and then you may have used this .gro as input to grompp and so your

run did not start with the exact same coordinates in gromacs and namd.

A similar test would be to be sure that you run grompp with the same

.pdb file that you used in namd, etc. (or perhaps you already did that?)



Actually, from what you post below I think that you have your answer.

Use the orig .pdb into grompp and things should be ok, probably even

in single precision, although the output .gro will be rounded as you

see.



PS: let's keep a positive mood.



Chris.


-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.


>>http://www.bio.cam.ac.uk/~awd28<<



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