date:20110425

[gmx-users] introducing ADP and ATP to Gromacs

2011-04-25 Thread Sajad Ahrari

dear users
is there any way to introduce "ADP" and "ATP" to Gromacs? my protein holds 
these 
ligands. but they are not known to Gromacs.
regards.
Sajad
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Re: [gmx-users] introducing ADP and ATP to Gromacs

2011-04-25 Thread Mark Abraham


On 4/25/2011 6:26 PM, Sajad Ahrari wrote:

dear users
is there any way to introduce "ADP" and "ATP" to Gromacs? my protein 
holds these ligands. but they are not known to Gromacs.


Some of the GROMACS force fields have ATP.

Otherwise, the advice here 
http://www.gromacs.org/Documentation/How-tos/Parameterization is 
appropriate.


Mark



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Re: [gmx-users] dealing with ATP

2011-04-25 Thread Sajad Ahrari

dear Justin

it seems that, ADP and ATP are not known to any of gromacs forcefields. but 
their topologies have been described in amber web site(as follows). should i be 
adding them to .tpr file of gromacs? if so, how can i access this file and is 
there any modification being needed in what amber has introduced? (or i have to 
just do something like copy and paste?)
all the best
sajad

topology for ADP:

002

R-ADENOSINE - with diphosphate linker
adp.db94
 adp  INT 1
 CORRECT OMIT DU   BEG
   0.0
1   DUMM  DUM 0000.0000.0000.0000.000
2   DUMM  DUM 1001.0000.0000.0000.000
3   DUMM  DUM 2101.000   90.0000.0000.000
4   O1B   O3M 3211.000   90.000  180.000   -0.9552
5   PBP M 4321.434   90.000  180.0001.3672
6   O2B   O3E 5431.574  107.490  -79.441   -0.9552
7   O3B   O3E 5431.518  118.007  165.990   -0.9552
8   O3A   OSM 5431.599  113.374  180.000   -0.6346
9   PAP M 6541.646  130.619   36.6241.4929
   10   O1A   O2E 7651.504  109.212  -90.234   -0.9474
   11   O2A   O2E 7651.526  108.570   40.323   -0.9474
   12   O5*   OSM 7651.585   97.173  157.726   -0.6579
   13   C5*   CTM 8761.445  122.292  -66.3170.0558
   14   H50   H1E 9871.059  109.484   27.5310.0679
   15   H51   H1E 9871.059  109.437  -92.4560.0679
   16   C4*   CTM 9871.477  113.286  147.5380.1065
   17   H40   H1E16981.059  105.768 -179.1780.1174
   18   O4*   OSS16   1391.482  106.235  -62.889   -0.3548
   19   C1*   CTB18   16   131.391  107.688  128.8040.0394
   20   H10   H2E19   18   161.059  109.468   91.2280.2007
   21   N9N*S19   18   161.552  105.091 -143.300   -0.0251
   22   C8CKB21   19   181.388  123.797   33.4340.2006
   23   H80   H5E22   21   191.078  131.047   -3.3890.1553
   24   N7NBS22   21   191.384  108.967  176.598   -0.6073
   25   C5CBS24   22   211.395  103.0210.7020.0515
   26   C6CAB25   24   221.412  128.288  178.2520.7009
   27   N6N2B26   25   241.333  125.907   -3.791   -0.9019
   28   H60   H E27   26   251.010  120.0102.8290.4115
   29   H61   H E27   26   251.009  120.014 -177.1670.4115
   30   N1NCS26   25   241.343  113.319  178.851   -0.7615
   31   C2CQB30   26   251.340  123.433   -1.6640.5875
   32   H2H5E31   30   261.077  120.022 -177.8750.0473
   33   N3NCS31   30   261.377  125.3792.123   -0.6997
   34   C4CBE33   31   301.300  108.242   -0.0350.3053
   35   C3*   CTM16   13   121.484  117.051   57.5810.2022
   36   H30   H1E35   16   131.059  117.939   24.8200.0615
   37   O3*   OHS35   16   131.407  108.509  149.908   -0.6541
   38   H3*   HOE37   35   160.967  109.470  163.2540.4376
   39   C2*   CTM35   16   131.607  102.425  -96.7150.0670
   40   H20   H1E39   35   161.059  115.086   78.1190.0972
   41   O2*   OHS39   35   161.398  114.943 -153.294   -0.6139
   42   H2*   HOE41   39   350.967  109.456  -41.6790.4186

IMPROPER
 C8   C4   N9   C1*
 C6   H60  N6   H61
 N7   N9   C8   H80
 N1   N3   C2   H2


topology for ATP:

002

R-ADENOSINE - with triphosphate linker
atp.db94
 atp  INT 1
 CORRECT OMIT DU   BEG
   0.0
1   DUMM  DUM 0001.000   90.000  180.0000.000
2   DUMM  DUM 1000.967   90.000  180.0000.000
3   DUMM  DUM 2100.967  109.443  180.0000.000
4   O1G   O3M 3211.086  160.811  148.238   -0.9526
5   PGP M 4321.379   92.848 -159.6811.2650
6   O2G   O3E 5431.417  116.381 -173.072   -0.9526
7   O3G   O3E 5431.443  104.744   40.954   -0.9526
8   O3B   OSM 5431.742   94.444  -63.733   -0.5322
9   PBP M 8531.512  135.464 -125.1761.3852
   10   O1B   O2E 9851.415  113.542  -28.935   -0.8894
   11   O2B   O2E 9851.617  103.881 -164.747   -0.8894
   12   O3A   OSM 9851.734   96.237   83.499   -0.5689
   13   PAP M12981.516  131.613 -127.4611.2532
   14   O1A   O2E13   1291.526  115.352  -92.892   -0.8799
   15   O2A   O2E13   1291.410  109.213   53.806   -0.87

Re: [gmx-users] openmm 3.0, opencl support

2011-04-25 Thread lina

Have you installed the

CUDA Toolkit 4.0 ?
I have never tried, just guessed.

lina

On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka  wrote:

> Hello,
>
> I'm interested in knowing the level of development about gromacs supporting
> the opencl framework language.
>
> I have read the manual about gromacs 4.5.4 that says that opencl is going
> to be supported in future versions. Yet, in the openmm website,
> the new version of openmm (3.0 that is) is supposed to support both cuda
> and opencl framework alongside gromacs:
> (https://simtk.org/project/xml/downloads.xml?group_id=161)
> "The current release of OpenMM and OpenMM-accelerated GROMACS enables
> acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards. "
>
> I downloaded gromacs 4.5.4, along with the openmm 3.0. The installation of
> the packages went fine, yet while trying to build the
> mdrun-gpu option giving the command:
>
> cmake -DGMX_OPENMM=ON
>
> the installation aborted with the error:
>
> CMake Error at cmake/FindCUDA.cmake:465 (message):
>   Specify CUDA_TOOLKIT_ROOT_DIR
> Call Stack (most recent call first):
>   CMakeLists.txt:434 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
>
> Since gromacs developers are working alongside openmm ones:
>
> 1) does gromacs support the opencl framework?
> 2) if the answer to the above is affirmative, what am I supposed to do, so
> as the compilation to succeed?
> 3) if the answer to the 1st question is negative, could you please be more
> specific about the context "future"?
>
> Thank you in advance,
> Nikos
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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Re: [gmx-users] dealing with ATP

2011-04-25 Thread Itamar Kass


ATP is well 'known' and used, just put attention to it protionation state.


Cheers,

Itamar


On 25/04/2011 8:05 PM, Sajad Ahrari wrote:


dear Justin
it seems that, ADP and ATP are not known to any of gromacs 
forcefields. but their topologies have been described in amber web 
site(as follows). should i be adding them to .tpr file of gromacs? if 
so, how can i access this file and is there any modification being 
needed in what amber has introduced? (or i have to just do something 
like copy and paste?)

all the best
sajad

topology for ADP:
002

R-ADENOSINE - with diphosphate linker
adp.db94
  adp  INT 1
  CORRECT OMIT DU   BEG
0.0
 1   DUMM  DUM 0000.0000.0000.0000.000
 2   DUMM  DUM 1001.0000.0000.0000.000
 3   DUMM  DUM 2101.000
  90.0000.0000.000
 4   O1B   O3M 3211.000   90.000  180.000   -0.9552
 5   PBP M 4321.434   90.000  180.0001.3672
 6   O2B   O3E 5431.574  107.490  -79.441   -0.9552
 7   O3B   O3E 5431.518  118.007  165.990   -0.9552
 8   O3A   OSM 5431.599  113.374  180.000   -0.6346
 9   PAP M 6541.646  130.619   36.6241.4929
10   O1A   O2E 7651.504  109.212  -90.234   -0.9474
11   O2A   O2E 7651.526  108.570   40.323   -0.9474
12   O5*   OSM 7651.585   97.173  157.726   -0.6579
13   C5*   CTM 8761.445  122.292  -66.3170.0558
14   H50   H1E 9871.059  109.484   27.5310.0679
15   H51   H1E 9871.059  109.437  -92.4560.0679

  16   C4*   CTM 9871.477  113.286  147.5380.1065
17   H40   H1E16981.059  105.768 -179.1780.1174
18   O4*   OSS16   1391.482  106.235  -62.889   -0.3548
19   C1*   CTB18   16   131.391  107.688  128.8040.0394
20   H10   H2E19   18   161.059  109.468   91.2280.2007
21   N9N*S19   18   161.552  105.091 -143.300   -0.0251
22   C8CKB21   19   181.388  123.797   33.4340.2006
23   H80   H5E22   21   191.078  131.047   -3.3890.1553
24   N7NBS22   21   191.384  108.967  176.598   -0.6073
25   C5CBS24   22   211.395  103.0210.7020.0515
26   C6CAB25   24   221.412  128.288  178.2520.7009
27   N6N2B26   25   241.333  125.907   -3.791   -0.9019
28   H60   H E27   26
  251.010  120.0102.8290.4115
29   H61   H E27   26   251.009  120.014 -177.1670.4115
30   N1NCS26   25   241.343  113.319  178.851   -0.7615
31   C2CQB30   26   251.340  123.433   -1.6640.5875
32   H2H5E31   30   261.077  120.022 -177.8750.0473
33   N3NCS31   30   261.377  125.3792.123   -0.6997
34   C4CBE33   31   301.300  108.242   -0.0350.3053
35   C3*   CTM16   13   121.484  117.051   57.5810.2022
36   H30   H1E35   16   131.059  117.939   24.8200.0615
37   O3*   OHS35   16   131.407  108.509  149.908   -0.6541
38   H3*   HOE37   35   160.967  109.470  163.2540.4376
39   C2*   CTM35   16   131.607  102.425  -96.7150.0670
40   H20   H1E39   35   161.059  115.086   78.119
   0.0972
41   O2*   OHS39   35   161.398  114.943 -153.294   -0.6139
42   H2*   HOE41   39   350.967  109.456  -41.6790.4186

IMPROPER
  C8   C4   N9   C1*
  C6   H60  N6   H61
  N7   N9   C8   H80
  N1   N3   C2   H2


topology for ATP:

002

R-ADENOSINE - with triphosphate linker
atp.db94
  atp  INT 1
  CORRECT OMIT DU   BEG
0.0
 1   DUMM  DUM 0001.000   90.000  180.0000.000
 2   DUMM  DUM 1000.967   90.000  180.0000.000
 3   DUMM  DUM 2100.967  109.443  180.0000.000
 4   O1G   O3M 3211.086  160.811  148.238   -0.9526
 5   PGP M 4321.379   92.848 -159.6811.2650
 6   O2G   O3E 5431.417  116.381 -173.072   -0.9526
 7   O3G
O3E 5431.443  104.744   40.954   -0.9526
 8   O3B   OSM 5431.742   94.444  -63.733   -0.5322
 9   PBP M 8531.512  135.464 -125.1761.3852
10   O1B   O2E 9851.415  113.542  -28.935   -0.8894
11   O2B   O2E 9851.617  103.881 -164.747   -0.8894
12   O3A   OSM 9851.734   96.237   83.499   -0.5689
13   PAP

Re: [gmx-users] dealing with ATP

2011-04-25 Thread Mark Abraham


On 4/25/2011 8:05 PM, Sajad Ahrari wrote:

dear Justin
it seems that, ADP and ATP are not known to any of gromacs 
forcefields. but their topologies have been described in amber web 
site(as follows). should i be adding them to .tpr file of gromacs? if 
so, how can i access this file and is there any modification being 
needed in what amber has introduced? (or i have to just do something 
like copy and paste?)


This is doable, but there's probably no automatic conversion software, 
because nobody's needed to do this so often that writing software was 
worthwhile. So you'll have to spend some time with the AMBER and GROMACS 
documentation, to learn how to do the conversion of the parameters and 
functions between different file formats.


Mark


all the best
sajad

topology for ADP:
002

R-ADENOSINE - with diphosphate linker
adp.db94
  adp  INT 1
  CORRECT OMIT DU   BEG
0.0
 1   DUMM  DUM 0000.0000.0000.0000.000
 2   DUMM  DUM 1001.0000.0000.0000.000
 3   DUMM  DUM 2101.000
  90.0000.0000.000
 4   O1B   O3M 3211.000   90.000  180.000   -0.9552
 5   PBP M 4321.434   90.000  180.0001.3672
 6   O2B   O3E 5431.574  107.490  -79.441   -0.9552
 7   O3B   O3E 5431.518  118.007  165.990   -0.9552
 8   O3A   OSM 5431.599  113.374  180.000   -0.6346
 9   PAP M 6541.646  130.619   36.6241.4929
10   O1A   O2E 7651.504  109.212  -90.234   -0.9474
11   O2A   O2E 7651.526  108.570   40.323   -0.9474
12   O5*   OSM 7651.585   97.173  157.726   -0.6579
13   C5*   CTM 8761.445  122.292  -66.3170.0558
14   H50   H1E 9871.059  109.484   27.5310.0679
15   H51   H1E 9871.059  109.437  -92.4560.0679

  16   C4*   CTM 9871.477  113.286  147.5380.1065
17   H40   H1E16981.059  105.768 -179.1780.1174
18   O4*   OSS16   1391.482  106.235  -62.889   -0.3548
19   C1*   CTB18   16   131.391  107.688  128.8040.0394
20   H10   H2E19   18   161.059  109.468   91.2280.2007
21   N9N*S19   18   161.552  105.091 -143.300   -0.0251
22   C8CKB21   19   181.388  123.797   33.4340.2006
23   H80   H5E22   21   191.078  131.047   -3.3890.1553
24   N7NBS22   21   191.384  108.967  176.598   -0.6073
25   C5CBS24   22   211.395  103.0210.7020.0515
26   C6CAB25   24   221.412  128.288  178.2520.7009
27   N6N2B26   25   241.333  125.907   -3.791   -0.9019
28   H60   H E27   26
  251.010  120.0102.8290.4115
29   H61   H E27   26   251.009  120.014 -177.1670.4115
30   N1NCS26   25   241.343  113.319  178.851   -0.7615
31   C2CQB30   26   251.340  123.433   -1.6640.5875
32   H2H5E31   30   261.077  120.022 -177.8750.0473
33   N3NCS31   30   261.377  125.3792.123   -0.6997
34   C4CBE33   31   301.300  108.242   -0.0350.3053
35   C3*   CTM16   13   121.484  117.051   57.5810.2022
36   H30   H1E35   16   131.059  117.939   24.8200.0615
37   O3*   OHS35   16   131.407  108.509  149.908   -0.6541
38   H3*   HOE37   35   160.967  109.470  163.2540.4376
39   C2*   CTM35   16   131.607  102.425  -96.7150.0670
40   H20   H1E39   35   161.059  115.086   78.119
   0.0972
41   O2*   OHS39   35   161.398  114.943 -153.294   -0.6139
42   H2*   HOE41   39   350.967  109.456  -41.6790.4186

IMPROPER
  C8   C4   N9   C1*
  C6   H60  N6   H61
  N7   N9   C8   H80
  N1   N3   C2   H2


topology for ATP:

002

R-ADENOSINE - with triphosphate linker
atp.db94
  atp  INT 1
  CORRECT OMIT DU   BEG
0.0
 1   DUMM  DUM 0001.000   90.000  180.0000.000
 2   DUMM  DUM 1000.967   90.000  180.0000.000
 3   DUMM  DUM 2100.967  109.443  180.0000.000
 4   O1G   O3M 3211.086  160.811  148.238   -0.9526
 5   PGP M 4321.379   92.848 -159.6811.2650
 6   O2G   O3E 5431.417  116.381 -173.072   -0.9526
 7   O3G
O3E 5431.443  104.744   40.954   -0.9526
 8   O3B   OSM 5431.742   94.444  -63.733   -0.5322
 9   PBP M 8531.512  135.464 -125.1761.3852

[gmx-users] trjcat eneconv time continuation

2011-04-25 Thread David Rodríguez

Hi,

I am dealing with a special case of trajectory concatenation: I have several
equilibration trajectories that their times are always restarted to 0, due
employing different force constants for positional restraints, but using the
output structure of the previous step as input anyway. Using trjcat, it
obviously works when you do:

trjcat -f traj1.xtc traj2.xtc traj3.xtc traj4.xtc traj5.xtc traj6.xtc -o
traj_all.xtc -settime

and you interactively introduce 'c' (continue) for each case (there are no
overlapping frames). I haven't found a way to continue the trajectory times
without using -settime (neither -cat nor -keeplast), with both versions
4.0.7 or 4.5. At the same time, I've tried to introduce the 'c' value in a
non-interactive way (as indicated in
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive)
when using -settime, but it doesn't recognize it.

I was wondering if there is a way to make the above mentioned command-line
to work non-interactively. The same applies for the eneconv tool when
concatenating .edr files.

Thanks in advance,

-- 

David Rodríguez Díaz, PhD Student
Fundación Pública Galega de Medicina Xenómica (SERGAS)
Santiago de Compostela (Spain)
http://webspersoais.usc.es/persoais/david.rodriguez.diaz

 
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[gmx-users] Re: error in g_x2top

2011-04-25 Thread Justin A. Lemkul



Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message there and ask that anything further 
be posted to the list.  See below for comments.


Zahra Kayani wrote:

Dear, Dr.Lemkul
command1:pdb2gmx -f shp2.pdb -o conf.gro it runs normally
then for g_x2top, I tried these focefield :
G53a5 GROMOS96 53a5 Forcefield (official distribution)
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
but for both of them this error was appeared, now what should I do?
error: Could only find a forcefield type for 7351 out of 8397 atoms
please,tell which forcefield can be helpful for me.


The .n2t files that come pre-packaged with these force fields are largely 
incomplete.  Further, g_x2top is designed for small molecules, and for anything 
complex, it may not be possible to define proper (non-conflicting) .n2t entries. 
 If you can get the topology via pdb2gmx, then you shouldn't have to do 
anything else.


-Justin


with regards
Zahra



--


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


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Re: [gmx-users] trjcat eneconv time continuation

2011-04-25 Thread Mark Abraham


On 4/25/2011 8:42 PM, David Rodríguez wrote:

Hi,

I am dealing with a special case of trajectory concatenation: I have 
several equilibration trajectories that their times are always 
restarted to 0, due employing different force constants for positional 
restraints, but using the output structure of the previous step as 
input anyway. Using trjcat, it obviously works when you do:


trjcat -f traj1.xtc traj2.xtc traj3.xtc traj4.xtc traj5.xtc traj6.xtc 
-o traj_all.xtc -settime


and you interactively introduce 'c' (continue) for each case (there 
are no overlapping frames). I haven't found a way to continue the 
trajectory times without using -settime (neither -cat nor -keeplast), 
with both versions 4.0.7 or 4.5. At the same time, I've tried to 
introduce the 'c' value in a non-interactive way (as indicated in 
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive) 
when using -settime, but it doesn't recognize it.


I was wondering if there is a way to make the above mentioned 
command-line to work non-interactively. The same applies for the 
eneconv tool when concatenating .edr files.


Unfortunately, the advice you'd get from people here on the topic of how 
to make such commands work non-interactively is already on the link you 
provided. You're more likely to get effective help if you say exactly 
what you did and how you observed "it doesn't recognize it".


Mark



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[gmx-users] tutorials of REMD

2011-04-25 Thread fancy2012


Dear GMX users,
Are there some tutorials guiding how to do REMD simulations using gromacs? 
Thanks very much!
 
All the best,
qinghua
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Re: [gmx-users] tutorials of REMD

2011-04-25 Thread Justin A. Lemkul




fancy2012 wrote:


Dear GMX users,
Are there some tutorials guiding how to do REMD simulations using 
gromacs? Thanks very much!
 


Google will tell you if there is any formal tutorial, otherwise a quick check of 
the Gromacs site turns up:


http://www.gromacs.org/Documentation/How-tos/REMD

-Justin


All the best,
qinghua



--


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


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Re: [gmx-users] trjcat eneconv time continuation

2011-04-25 Thread David Rodríguez

2011/4/25 Mark Abraham 

> On 4/25/2011 8:42 PM, David Rodríguez wrote:
>
>> Hi,
>>
>> I am dealing with a special case of trajectory concatenation: I have
>> several equilibration trajectories that their times are always restarted to
>> 0, due employing different force constants for positional restraints, but
>> using the output structure of the previous step as input anyway. Using
>> trjcat, it obviously works when you do:
>>
>> trjcat -f traj1.xtc traj2.xtc traj3.xtc traj4.xtc traj5.xtc traj6.xtc -o
>> traj_all.xtc -settime
>>
>> and you interactively introduce 'c' (continue) for each case (there are no
>> overlapping frames). I haven't found a way to continue the trajectory times
>> without using -settime (neither -cat nor -keeplast), with both versions
>> 4.0.7 or 4.5. At the same time, I've tried to introduce the 'c' value in a
>> non-interactive way (as indicated in
>> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive)
>> when using -settime, but it doesn't recognize it.
>>
>> I was wondering if there is a way to make the above mentioned command-line
>> to work non-interactively. The same applies for the eneconv tool when
>> concatenating .edr files.
>>
>
> Unfortunately, the advice you'd get from people here on the topic of how to
> make such commands work non-interactively is already on the link you
> provided. You're more likely to get effective help if you say exactly what
> you did and how you observed "it doesn't recognize it".
>

Sorry that my query wasn't detailed enough. Trjcat yields a Fatal error
(Error reading user input). Here is what I tried, considering the first 2
trajectories (the errors are the same if you consider more than that):

Option 1:
echo c | trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime

Option 2:
trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime << EOF
c
EOF

Option 3:
trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime < choice.txt

Where 'choice.txt' contains the letter 'c' in one line.
The log in any case is the following:



  :-)  /opt/gromacs405/bin/trjcat  (-:

Option Filename  Type Description

  -f  traj1.xtc  Input, Mult.
  traj2.xtc   Trajectory: xtc trr trj gro g96 pdb cpt
  -o   traj_1_2.xtc  Output, Mult. Trajectory: xtc trr trj gro g96 pdb
  -n  index.ndx  Input, Opt.  Index file
-demux remd.xvg  Input, Opt.  xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-tu  enum   ps  Time unit: ps, fs, ns, us, ms or s
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-b   time   -1  First time to use (ps)
-e   time   -1  Last time to use (ps)
-dt  time   0   Only write frame when t MOD dt = first time (ps)
-precint3   Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool   yes Read and write velocities if possible
-[no]settime bool   yes Change starting time interactively
-[no]sortbool   yes Sort trajectory files (not frames)
-[no]keeplast  bool no  keep overlapping frames at end of trajectory
-[no]cat bool   no  do not discard double time frames

Reading frame   1 time   50.000


Enter the new start time (ps) for each file.
There are two special options, both disable sorting:

c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
restarts with t=0.

l (last) - The time in this file will be changed the
same amount as in the previous. Use it when the time in the
new run continues from the end of the previous one,
since this takes possible overlap into account.

  File Current start (ps)  New start (ps)
-
traj1.xtc0.000 ps
traj2.xtc0.000 ps
---
Program trjcat, VERSION 4.0.5
Source code file: gmx_trjcat.c, line: 178

Fatal error:
Error reading user input
---

"Yeah, a Wuzz, Or a Jerk" (F. Black)



This is with version 4.0.5, when using version 4.5 the log only differs in
the line of the code where the error occurs (201 instead of 178).

Best,
David.


> Mark
>
>
>
> --
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Re: [gmx-users] openmm 3.0, opencl support

2011-04-25 Thread Claus Valka

Hello,

thank you for your prompt response. Unfortunately neither cuda toolkit 3.2 nor 
4.0 was possible to be installed on my system. It required nvidia.co file. I 
think I just have to wait for an ati-opencl gromacs support.

Regards,
Nikos



Von: lina 
An: Claus Valka ; Discussion list for GROMACS users 

Gesendet: 13:19 Montag, 25.April 2011 
Betreff: Re: [gmx-users] openmm 3.0, opencl support


Have you installed the 


CUDA Toolkit 4.0 ?
I have never tried, just guessed. 

lina


On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka  wrote:

Hello,
>
>I'm interested in knowing the level of development about gromacs supporting 
>the opencl framework language. 
>
>I have read the manual about gromacs 4.5.4 that says that opencl is going to 
>be supported in future versions. Yet, in the openmm website,
>the new version of openmm (3.0 that is) is supposed to support both cuda and 
>opencl framework alongside gromacs:
>(https://simtk.org/project/xml/downloads.xml?group_id=161)
>"The current release of OpenMM and OpenMM-accelerated GROMACS enables 
acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards.
  "
>
>I downloaded gromacs 4.5.4, along with the openmm 3.0. The installation of the 
>packages went fine, yet while trying to build the
>mdrun-gpu option giving the command:
>
>cmake -DGMX_OPENMM=ON
>
>the installation aborted with the error:
>
>CMake Error at cmake/FindCUDA.cmake:465 (message):
>  Specify CUDA_TOOLKIT_ROOT_DIR
>Call Stack (most recent call first):
>  CMakeLists.txt:434 (find_package)
>
>
>-- Configuring incomplete, errors occurred!
>
>Since gromacs developers are working alongside openmm ones:
>
>1) does gromacs support the opencl framework?
>2) if the answer to the above is affirmative, what am I supposed to do, so as 
>the compilation to succeed?
>3) if the answer to the 1st question is negative, could you please be more 
>specific about the context "future"?
>
>Thank you in
 advance,
>Nikos
>
>
>
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Re: [gmx-users] trjcat eneconv time continuation

2011-04-25 Thread Tsjerk Wassenaar

Hi David,

You should have as many lines with a 'c' as you have trajectories.

Cheers,

Tsjerk

On Apr 25, 2011 3:51 PM, "David Rodríguez" 
wrote:



2011/4/25 Mark Abraham  > > On 4/25/2011 8:42 PM,
David Rodríguez wrote: >>...

Sorry that my query wasn't detailed enough. Trjcat yields a Fatal error
(Error reading user input). Here is what I tried, considering the first 2
trajectories (the errors are the same if you consider more than that):

Option 1:
echo c | trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime

Option 2:
trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime << EOF
c
EOF

Option 3:
trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime < choice.txt

Where 'choice.txt' contains the letter 'c' in one line.
The log in any case is the following:



  :-)  /opt/gromacs405/bin/trjcat  (-:

Option Filename  Type Description

  -f  traj1.xtc  Input, Mult.
  traj2.xtc   Trajectory: xtc trr trj gro g96 pdb cpt
  -o   traj_1_2.xtc  Output, Mult. Trajectory: xtc trr trj gro g96 pdb
  -n  index.ndx  Input, Opt.  Index file
-demux remd.xvg  Input, Opt.  xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-tu  enum   ps  Time unit: ps, fs, ns, us, ms or s
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-b   time   -1  First time to use (ps)
-e   time   -1  Last time to use (ps)
-dt  time   0   Only write frame when t MOD dt = first time (ps)
-precint3   Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool   yes Read and write velocities if possible
-[no]settime bool   yes Change starting time interactively
-[no]sortbool   yes Sort trajectory files (not frames)
-[no]keeplast  bool no  keep overlapping frames at end of trajectory
-[no]cat bool   no  do not discard double time frames

Reading frame   1 time   50.000


Enter the new start time (ps) for each file.
There are two special options, both disable sorting:

c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
restarts with t=0.

l (last) - The time in this file will be changed the
same amount as in the previous. Use it when the time in the
new run continues from the end of the previous one,
since this takes possible overlap into account.

  File Current start (ps)  New start (ps)
-
traj1.xtc0.000 ps
traj2.xtc0.000 ps
---
Program trjcat, VERSION 4.0.5
Source code file: gmx_trjcat.c, line: 178

Fatal error:
Error reading user input
---

"Yeah, a Wuzz, Or a Jerk" (F. Black)



This is with version 4.0.5, when using version 4.5 the log only differs in
the line of the code where the error occurs (201 instead of 178).

Best,
David.

> > Mark > > > > -- > gmx-users mailing listgmx-users@gromacs.org >
http://lists.gromacs.org/ma...





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Re: [gmx-users] trjcat eneconv time continuation

2011-04-25 Thread David Rodríguez

2011/4/25 Tsjerk Wassenaar 

> Hi David,
>
> You should have as many lines with a 'c' as you have trajectories.
>
> Cheers,
>
> Tsjerk
>
Sure Tsjerk!

Now options 2 and 3 (not 1) work, just that easy. Thank you so much.

Best,
David.

> On Apr 25, 2011 3:51 PM, "David Rodríguez" 
> wrote:
>
>
>
> 2011/4/25 Mark Abraham  > > On 4/25/2011 8:42 PM,
> David Rodríguez wrote: >>...
>
> Sorry that my query wasn't detailed enough. Trjcat yields a Fatal error
> (Error reading user input). Here is what I tried, considering the first 2
> trajectories (the errors are the same if you consider more than that):
>
> Option 1:
> echo c | trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime
>
> Option 2:
> trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime << EOF
> c
> EOF
>
> Option 3:
> trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime < choice.txt
>
> Where 'choice.txt' contains the letter 'c' in one line.
> The log in any case is the following:
>
>
>
>   :-)  /opt/gromacs405/bin/trjcat  (-:
>
> Option Filename  Type Description
> 
>   -f  traj1.xtc  Input, Mult.
>   traj2.xtc   Trajectory: xtc trr trj gro g96 pdb cpt
>   -o   traj_1_2.xtc  Output, Mult. Trajectory: xtc trr trj gro g96 pdb
>   -n  index.ndx  Input, Opt.  Index file
> -demux remd.xvg  Input, Opt.  xvgr/xmgr file
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -niceint19  Set the nicelevel
> -tu  enum   ps  Time unit: ps, fs, ns, us, ms or s
> -[no]xvgrbool   yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -b   time   -1  First time to use (ps)
> -e   time   -1  Last time to use (ps)
> -dt  time   0   Only write frame when t MOD dt = first time
> (ps)
> -precint3   Precision for .xtc and .gro writing in number
> of
> decimal places
> -[no]vel bool   yes Read and write velocities if possible
> -[no]settime bool   yes Change starting time interactively
> -[no]sortbool   yes Sort trajectory files (not frames)
> -[no]keeplast  bool no  keep overlapping frames at end of trajectory
> -[no]cat bool   no  do not discard double time frames
>
> Reading frame   1 time   50.000
>
>
> Enter the new start time (ps) for each file.
> There are two special options, both disable sorting:
>
> c (continue) - The start time is taken from the end
> of the previous file. Use it when your continuation run
> restarts with t=0.
>
> l (last) - The time in this file will be changed the
> same amount as in the previous. Use it when the time in the
> new run continues from the end of the previous one,
> since this takes possible overlap into account.
>
>   File Current start (ps)  New start (ps)
> -
> traj1.xtc0.000 ps
> traj2.xtc0.000 ps
> ---
> Program trjcat, VERSION 4.0.5
> Source code file: gmx_trjcat.c, line: 178
>
> Fatal error:
> Error reading user input
> ---
>
> "Yeah, a Wuzz, Or a Jerk" (F. Black)
>
>
>
> This is with version 4.0.5, when using version 4.5 the log only differs in
> the line of the code where the error occurs (201 instead of 178).
>
> Best,
> David.
>
> > > Mark > > > > -- > gmx-users mailing listgmx-users@gromacs.org >
> http://lists.gromacs.org/ma...
>
>
>
>
>
> --
>
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>
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Re: [gmx-users] trjcat eneconv time continuation

2011-04-25 Thread Tsjerk Wassenaar

Hi David,

Sorry for reading half... 'echo c c | trjcat ... ' should work.

Cheers,

Tsjerk

On Apr 25, 2011 6:02 PM, "David Rodríguez" 
wrote:


2011/4/25 Tsjerk Wassenaar  > > Hi David, > > You should
have as many lines with ...
Sure Tsjerk!

Now options 2 and 3 (not 1) work, just that easy. Thank you so much.

Best,
David.

>> >> On Apr 25, 2011 3:51 PM, "David Rodríguez" 
wrote: >> >> >> >> 201...




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[gmx-users] Load imbalance vs accuracy

2011-04-25 Thread Sikandar Mashayak

Hi

Is load imbalance during mdrun only a performance issue or it affects
accuracy of run as well?

thanks
sikandar
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[gmx-users] Re: Potential energy methanol in a box

2011-04-25 Thread Fabian Casteblanco

Thanks again for your response.  I appreciate all your help.

On Sat, Apr 23, 2011 at 6:11 PM, Fabian Casteblanco
 wrote:
> Hello,
>
> I'm trying to fill a box with methanol using CHARMM FF Parameters.  I
> also need to do this for ethanol and 1-propanol.
>
> For ethanol, each individual molecule had approximately -19 kJ/mol of
> potential energy, then I placed 1000 in a box, performed nvt, npt,
> etc.  End Result:  A negative potential energy (it means that its
> stable?)  and a density of 0.785 g/cm3 compared to actual 0.789 g/cm3
> at 1 atm, 298 K.  This result seemed ok.
>
> For methanol and  1-propanol, each individual molecule had a larger
> 24 - 64 kJ/mol respectively, due to Coulomb 1,4 pair interactions (for
> example, for methanol between the HA 0.09 and the H 0.43 gives a large
> 64 kJ/mol).  Again placed 1000 each in 2 separate boxes, performed
> nvt,npt,etc on each one.  End Result:  A still positive potential
> energy for each box (shouldn't this be negative after running npt? on
> both) and a density that was 0.789 g/cm3 (for 1-propanol)compared to
> actual 0.803 g/cm3 1-propanol at 1 atm, 298 K.  Methanol density a bit
> closer 0.787 compared to 0.791 g/cm3.
>
> My questions are:
> -There should definetly be a positive potential energy after running
> npt, correct? Otherwise it wouldn't be stable?  I understand that the
> 1,4 coulomb interactions should cancel out with nearby molecules.
> *For CHARMM, they state that unless otherwise 1,4 parameters exist
> already, they use a full scale 1.0 of the regular LJ, coulomb
> potential.
>
> -As for the density, I know it's somewhat close but I'm trying to be
> as accurate as possible.  I read somewhere that the average cut-off
> (rlist) is usually 1.4 for CHARMM and I had mine set to 1.  I'm
> guessing that having a larger cutoff would contribute more molecules
> to the LJ, coulomb which might rise the density a bit to the correct
> value?
>
> I'm still new to Gromacs so I appreciate all of anybodys help.  Thanks a 
> bunch.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
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Re: [gmx-users] Load imbalance vs accuracy

2011-04-25 Thread Roland Schulz

Hi,

load imbalance is only a performance issue.

Load balancing affects binary reproducibility (meaning the exact same value)
but not accuracy (those it can differ but only within the same accuracy).
Binary reproducibility should only be important for testing purposes, thus
you should use load balancing to improve the performance if you have
a significant imbalance.

Roland

On Mon, Apr 25, 2011 at 2:17 PM, Sikandar Mashayak wrote:

> Hi
>
> Is load imbalance during mdrun only a performance issue or it affects
> accuracy of run as well?
>
> thanks
> sikandar
>
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