[gmx-users] virtusal site setting

[라지브간디]

Dear Richard,


For instance, To simulate the hemoglobin with heme ligated CO, would like to 
set the charges on center of mass of CO. 


How do i include the virtual sites atom in co-ordinates (x,y and z)?. I added 
the virtual sites line in topology as follows:


[ moleculetype ]
; molname   nrexcl
CMO 2


[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   OM  1   CMO O 1  -0.8515.9994
2   CM  1   CMO C 1  -0.7512.0110
3   COM1   CMO M11.60 0.000


[ bonds ]
; i j   funct   length  force.c.
1   2   1  0.1128  933032.0


[ virtual_sites2 ]
; Vsite from  funct   a   
3   1   2   1   0.042880515






Also, i entered in .atp and .rtp file. Could you please give some procedure to 
do this? Thanks in advance.




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, "��"  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 

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Re: [gmx-users] Freezing group

[Justin Lemkul]

On 3/28/13 4:24 PM, Алексей Раевский wrote:

Hi dear All!
Good day dear forum! I have a question abour freezing of atoms during MD.
The idea is that - I have a protein and one domain contains a site. Also I
have two ligands, one of them is better inhibitor in comparison with
another one. To prepare the topology of the inhibitor I need to use a
R.E.D.III server. As there are several different fitting methods, so I have
to carry out a series of short MDs (about 5-10 ns) for each of them. The
question is - is it possible to isolate this domain and fix/freeze last
residues of the hairpin/linker to prevent movement of domain segments? I
know that this is not the way to study ligand-protein interaction, however
I just want to use it for understanding which topology generation method is
better.


You can freeze whatever group you want using freezegrps and a custom index 
group.  It is also reasonably simple to restrain a segment of the structure 
using normal position restraints (again, created with a custom index group).


-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


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[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

[Christopher Neale]

Thank you, Berk, Justin, and Matthew, for your assistance.

I checked with my sysadmin, who said:

The /global/scratch FS is Lustre. It is fully POSIX and the fsync etc 
are fully and well implemented. However when the 'power off' command is 
issued there is no way OS can finish I/O in a controlled way.

Note that the power off command was given when they
realized that they had lost all cooling in the data room, and they had just a 
few 
minutes to react, forcing them to shutdown all compute nodes. 

Justin's suggestion to use  -cpnum is good, although I think it will be easier 
to simply have a script that runs 
gmxcheck once every 12 hours and backs up the .cpt file if it is ok.

I don't know enough about computer OS's to say if there is any possible way for 
gromacs to avoid this
in the future, but if it was possible, then it would be useful.

Thank you again,
Chris.

-- original message --

Gromacs calls fsync for every checkpoint file written:

   fsync() transfers ("flushes") all modified in-core data of (i.e., modi-
   fied  buffer cache pages for) the file referred to by the file descrip-
   tor fd to the disk device (or other permanent storage device)  so  that
   all  changed information can be retrieved even after the system crashed
   or was rebooted.  This includes writing  through  or  flushing  a  disk
   cache  if  present.   The call blocks until the device reports that the
   transfer has completed.  It also flushes metadata  information  associ-
   ated with the file (see stat(2)).

If fsync fails, mdrun exits with a fatal error.
We have experience with unreliable AFS file systems, where fsync mdrun could 
wait for hours and fail,
for which we added an environment variable.
So either fsync is not supported on your system (highly unlikely)
or your file system returns 0, indicating the file was synched, but it actually 
didn't fully sync.

Note that we first write a new checkpoint file with number, fynsc that, then 
move the current
to _prev (thereby loosing the old prev) and then the numbered one to the 
current.
So you should never end up with only corrupted files, unless fsync doesn't do 
what it's supposed to do.

Cheers,

Berk

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Re: [gmx-users] RE: diffusion constant level off

[Justin Lemkul]

On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote:

The simplest advice is to increase sampling.



I think the OP needs to describe what the system is in greater detail.  For a 
simple liquid, I would opine that 200 ns is normally vast overkill.  For a 
membrane, it may not be enough.  There's just no way to say.


-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


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Re: [gmx-users] Re: diffusion constant level off

[Justin Lemkul]

On 3/28/13 5:32 PM, Ahmet yıldırım wrote:

Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/



How did you come up with your "expected" values?  What does the original msd.xvg 
plot look like?  It should be basically linear.  If it's not, then you have 
found the source of your problem.


-Justin


2013/3/28 Justin Lemkul 


On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım 
wrote:


Dear users,

Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?



I see no evidence for a bug, and you should avoid such speculation unless
you know exactly how the program should behave. Only then, after an
analysis of known quantities or behavior, can we discuss bugginess. Do you
know how g_msd works? Do you know what all of the flags are doing, or are
you just making adjustments hoping for clarity? You may find the following
post very illuminating:

http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html

-Justin



Commands for trestart to 20 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
-endfit -1 -b 1 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
-endfit -1 -b 2 -e 3
...
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
-endfit -1 -b 19 -e 20

Commands for trestart to 1000 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 1 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 2 -e 3
...
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 19 -e 20


D1 (cm^2/s):Diffusion for trestart to 20 ps
D2 (cm^2/s):Diffusion for trestart to 1000 ps
Time (ns) D1 D2
10 0.1616 0.1091
20 0.0735 0.0679
30 0.0775 0.0705
40 0.1097 0.1189
50 0.1471 0.1436
60 0.0468 0.048
70 0.0667 0.0652
80 0.0727 0.086
90 0.0664 0.0707
100 0.1336 0.114
110 0.0899 0.0841
120 0.0572 0.0598
130 0.0506 0.0482
140 0.0723 0.0767
150 0.1466 0.1439
160 0.0703 0.0601
170 0.081 0.0853
180 0.0278 0.027
190 0.1121 0.1024
200 0.3136 0.2981


2013/3/28 Dr. Vitaly Chaban 




if I do as you said, I will get only one diffusion coefficient. I

want

to

calculate one diffusion coefficient for each 10
ns of the simulation time of 200 ns. That is, I want to get 20

diffusion

values.

2013/3/28 David van der Spoel 


On 2013-03-28 10:40, Ahmet yıldırım wrote:


Dear users,

This time, I calculated the diffusion coefficients of protein for

each 10

ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit

-1

-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit

-1

-endfit -1 -b 10001 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit

-1

-endfit -1 -b 20001 -e 3

g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit

-1

-endfit -1 -b 190001 -e 20



Set trestart to 10001 (no restarts), or do one run with

g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1




I believe the advice was to increase "trestart" and you can decide
yourself how much to increase.

Most likely, your protein deserves better sampling than 10 ns for a
linear diffusion.

Dr. Vitaly Chaban
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Ahmet Yıldırım
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--



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


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Re: [gmx-users] TOP file question

[Justin Lemkul]

On 3/28/13 8:25 PM, Peter Eastman wrote:

After further study of the documentation, I find myself getting more confused rather than 
less.  I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not 
Coulomb parameters.  (There's a function type 2 for [pairs] that does include charges, 
but the manual says that function type is only used for free energy calculations.)  How 
do I select the latter when gen-pairs is off?  Is it simply assumed that 1-4 Coulomb 
interactions are never reduced for force fields that don't use gen-pairs?  Table 5.5 
lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as 
LJ.  But no other mention of this directive appears anywhere else in the manual, there 
doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that 
"pairs_nb" never occurs in any file in the entire top directory.

What am I misunderstanding?



Which version of the manual are you using?  I recall the discussion on 
[pairs_nb] being absent in an older version, but manual section 5.3.4 in version 
4.6.1 has lots of discussion on [pairs_nb].


-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


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Re: [gmx-users] TOP file question

[Justin Lemkul]

On 3/28/13 7:14 PM, Peter Eastman wrote:

3. If gen-pairs is "yes", then generate parameters for all 1-2, 1-3, and 1-4 
pairs for which we did not already find parameters in step 1 or 2 (regardless of whether 
or not a [pairs] line exists for a particular pair).


Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a [pairs] 
record for each 1-4.



Not quite.  The presence of an entry in [pairs] is required.  When processing 
the topology, grompp doesn't do any magic.  It won't generate pair interactions 
for any combination for which there is no entry.  I think "gen-pairs" is 
somewhat misleading.  It doesn't generate pairs.  It generates parameters for 
the pairs that the user (or pdb2gmx/g_x2top) has listed, which assumes proper 
use of the force field.


For a bit more discussion of how this all works:

http://lists.gromacs.org/pipermail/gmx-users/2012-December/077005.html

-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


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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

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Re: [gmx-users] TOP file question

[Peter Eastman]

After further study of the documentation, I find myself getting more confused 
rather than less.  I see that the [pairs] and [pairtypes] directives only 
specify LJ parameters, not Coulomb parameters.  (There's a function type 2 for 
[pairs] that does include charges, but the manual says that function type is 
only used for free energy calculations.)  How do I select the latter when 
gen-pairs is off?  Is it simply assumed that 1-4 Coulomb interactions are never 
reduced for force fields that don't use gen-pairs?  Table 5.5 lists an 
alternate directive, [pairs_nb] that does specify Coulomb parameters as well as 
LJ.  But no other mention of this directive appears anywhere else in the 
manual, there doesn't seem to be any corresponding [pairtypes] option, and a 
grep reveals that "pairs_nb" never occurs in any file in the entire top 
directory.

What am I misunderstanding?

Peter--
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[gmx-users] RE: diffusion constant level off

[Dr. Vitaly Chaban]

The simplest advice is to increase sampling.



> Please see plot:

> http://imageshack.us/photo/my-images/35/diffusion.png/
>
> 2013/3/28 Justin Lemkul 
>
> > On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım 
> > wrote:
> >
> > > Dear users,
> > >
> > > Again, I have strange results (for 10,50,100,150,200 ns). I am
> wondering,
> > > is there a bug with g_msd?
> > >
> > >
> > I see no evidence for a bug, and you should avoid such speculation unless
> > you know exactly how the program should behave. Only then, after an
> > analysis of known quantities or behavior, can we discuss bugginess. Do
> you
> > know how g_msd works? Do you know what all of the flags are doing, or are
> > you just making adjustments hoping for clarity? You may find the
> following
> > post very illuminating:
> >
> > http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html
> >
> > -Justin
> >
> >
> > > Commands for trestart to 20 ps:
> > > g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
> > > -endfit -1 -b 0 -e 1
> > > g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
> > > -endfit -1 -b 1 -e 2
> > > g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
> > > -endfit -1 -b 2 -e 3
> > > ...
> > > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> > > -endfit -1 -b 19 -e 20
> > >
> > > Commands for trestart to 1000 ps:
> > > g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
> > > -endfit -1 -b 0 -e 1
> > > g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
> > > -endfit -1 -b 1 -e 2
> > > g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
> > > -endfit -1 -b 2 -e 3
> > > ...
> > > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
> > > -endfit -1 -b 19 -e 20
> > >
> > >
> > > D1 (cm^2/s):Diffusion for trestart to 20 ps
> > > D2 (cm^2/s):Diffusion for trestart to 1000 ps
> > > Time (ns) D1 D2
> > > 10 0.1616 0.1091
> > > 20 0.0735 0.0679
> > > 30 0.0775 0.0705
> > > 40 0.1097 0.1189
> > > 50 0.1471 0.1436
> > > 60 0.0468 0.048
> > > 70 0.0667 0.0652
> > > 80 0.0727 0.086
> > > 90 0.0664 0.0707
> > > 100 0.1336 0.114
> > > 110 0.0899 0.0841
> > > 120 0.0572 0.0598
> > > 130 0.0506 0.0482
> > > 140 0.0723 0.0767
> > > 150 0.1466 0.1439
> > > 160 0.0703 0.0601
> > > 170 0.081 0.0853
> > > 180 0.0278 0.027
> > > 190 0.1121 0.1024
> > > 200 0.3136 0.2981
> > >
> > >
> > > 2013/3/28 Dr. Vitaly Chaban 
> > > >
> > > > >
> > > > > if I do as you said, I will get only one diffusion coefficient. I
> > want
> > > to
> > > > > calculate one diffusion coefficient for each 10
> > > > > ns of the simulation time of 200 ns. That is, I want to get 20
> > > diffusion
> > > > > values.
> > > > >
> > > > > 2013/3/28 David van der Spoel 
> > > > >
> > > > >> On 2013-03-28 10:40, Ahmet yıldırım wrote:
> > > > >>
> > > > >>> Dear users,
> > > > >>>
> > > > >>> This time, I calculated the diffusion coefficients of protein for
> > > each 10
> > > > >>> ns of the simulation providing a total simulation time of 200 ns.
> > > > >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit
> > -1
> > > > >>> -endfit -1 -b 0 -e 1
> > > > >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit
> > -1
> > > > >>> -endfit -1 -b 10001 -e 2
> > > > >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit
> > -1
> > > > >>> -endfit -1 -b 20001 -e 3
> > > > >>> 
> > > > >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20
> -beginfit
> > -1
> > > > >>> -endfit -1 -b 190001 -e 20
> > > > >>>
> > > > >>
> > > > >> Set trestart to 10001 (no restarts), or do one run with
> > > > >>
> > > > >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
> > > > >>
> > > >
> > > >
> > > > I believe the advice was to increase "trestart" and you can decide
> > > > yourself how much to increase.
> > > >
> > > > Most likely, your protein deserves better sampling than 10 ns for a
> > > > linear diffusion.
> > > >
> > > > Dr. Vitaly Chaban
>
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Re: [gmx-users] TOP file question

[Peter Eastman]

> 3. If gen-pairs is "yes", then generate parameters for all 1-2, 1-3, and 1-4 
> pairs for which we did not already find parameters in step 1 or 2 (regardless 
> of whether or not a [pairs] line exists for a particular pair).

Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a [pairs] 
record for each 1-4.

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Re: [gmx-users] no CUDA-capable device is detected

[Szilárd Páll]

Hi,

I'm glad that it got figured out. For all those who might be wondering what
exactly are you referring to here is a quick summary.

The NVIDIA driver needs /dev entries to be present for the GPU devices in
use and these entries need the right permissions in order to allow
user-space programs to access the devices (and the lack of permission was
causing trouble in the above case). These entries are automatically created
by the X server and the driver kernel module is also loaded when X starts.
However, when using a headless (i.e server/without X) installation, what's
otherwise automatically done by when X starts needs to be done manually. It
is easiest to do it using an init script (or equivalent).

For an example here's the init script I use on Ubuntu machines:
http://pastebin.com/zs9Ve9qP. It works for me well, but use it at your own
risk ;)

Cheers,

--
Szilárd


On Thu, Mar 28, 2013 at 12:03 PM, Chandan Choudhury wrote:

> Hi !!
>
> I problem with the permission of /dev/nvidia*
>
> changed it to 0666 /dev/nvidia*
>
> Everything resolved. mdrun  can be executed as normal user.
>
> Thanks everyone.
>
> Chandan
>
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury  >wrote:
>
> >
> > On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll  >wrote:
> >
> >> Hi,
> >>
> >> If mdrun says that it could not detect GPUs it simply means that the GPU
> >> enumeration found no GPUs, otherwise it would have printed what was
> found.
> >> This is rather strange because mdrun uses the same mechanism the
> >> deviceQuery SDK example. I really don't have a good idea what could be
> the
> >> issue, but you could try recompiling or compiling with CUDA 4.2 to see
> if
> >> any of that makes a difference.
> >>
> >> Let us know if you figured out something.
> >>
> >> Cheers,
> >>
> >
> > Thanks Szilárd for the eye opening comment.
> >
> > I just tried running gromacs as root. I recalled I had executed
> > deviceQuery as root. While executing as user it produces the same error :
> >
> > */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery
> > Starting...
> >
> >  CUDA Device Query (Runtime API) version (CUDART static linking)
> >
> > cudaGetDeviceCount returned 38
> > -> no CUDA-capable device is detected*
> >
> > Now, running gromacs as root, it is running successfully (I suppose).
> >
> > Output of nvidia-smi
> >
> >
> > +--+
> >
> > | NVIDIA-SMI 4.310.40   Driver Version: 310.40
> > |
> >
> >
> |---+--+--+
> > | GPU  Name | Bus-IdDisp.  | Volatile Uncorr.
> > ECC |
> > | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util
>  Compute
> > M. |
> >
> >
> |===+==+==|
> > |   0  NVS 300  | :03:00.0 N/A |
> > N/A |
> > | N/A   48C  N/A N/A /  N/A |   3%   17MB /  511MB | N/A
> > Default |
> >
> >
> >
> +---+--+--+
> > |   1  Tesla K20c   | :04:00.0 Off |
> > Off |
> > | 50%   62CP0   106W / 225W |   2%   87MB / 5119MB | 76%
> > Default |
> >
> >
> >
> +---+--+--+
> >
> >
> >
> >
> +-+
> > | Compute processes:   GPU
> > Memory |
> > |  GPU   PID  Process name
> > Usage  |
> >
> >
> |=|
> > |0Not
> > Supported   |
> > |1  9127  mdrun_461
> > 72MB  |
> >
> >
> +-+
> >
> > Output of md.log
> >
> > 2 GPUs detected:
> >   #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC:  no, stat: compatible
> >   #1: NVIDIA NVS 300, compute cap.: 1.2, ECC:  no, stat: incompatible
> >
> > 1 GPU auto-selected for this run: #0
> >
> >
> > I think there is something relate to permissions. Though nvcc has 755
> > permission, something else might require additional permissions.
> >
> > Chandan
> >
> >
> >> --
> >> Szilárd
> >>
> >>
> >> On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess  wrote:
> >>
> >> >
> >> > Hi,
> >> >
> >> > I am not the expert on GPU detection, so we'll need to wait until an
> >> > expert replies.
> >> > Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
> >> > mdrun -ntmpi 1 -gpu_id 0
> >> >
> >> > Also your tpr file is from an older version. It will not run on a GPU.
> >> > You need to set the mdp option:
> >> > cutoff-scheme = Verlet
> >> > and run grompp to get a new tpr file.
> >> >
> >> > Cheers,
> >> >
> >> > Berk
> >> >
> >> > > From: iitd...@gmail.com
> >> > > Date: Thu, 28 Mar 2013 14:57:16 +0

Re: [gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/

2013/3/28 Justin Lemkul 

> On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım 
> wrote:
>
> > Dear users,
> >
> > Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
> > is there a bug with g_msd?
> >
> >
> I see no evidence for a bug, and you should avoid such speculation unless
> you know exactly how the program should behave. Only then, after an
> analysis of known quantities or behavior, can we discuss bugginess. Do you
> know how g_msd works? Do you know what all of the flags are doing, or are
> you just making adjustments hoping for clarity? You may find the following
> post very illuminating:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html
>
> -Justin
>
>
> > Commands for trestart to 20 ps:
> > g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
> > -endfit -1 -b 0 -e 1
> > g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
> > -endfit -1 -b 1 -e 2
> > g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
> > -endfit -1 -b 2 -e 3
> > ...
> > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> > -endfit -1 -b 19 -e 20
> >
> > Commands for trestart to 1000 ps:
> > g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
> > -endfit -1 -b 0 -e 1
> > g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
> > -endfit -1 -b 1 -e 2
> > g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
> > -endfit -1 -b 2 -e 3
> > ...
> > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
> > -endfit -1 -b 19 -e 20
> >
> >
> > D1 (cm^2/s):Diffusion for trestart to 20 ps
> > D2 (cm^2/s):Diffusion for trestart to 1000 ps
> > Time (ns) D1 D2
> > 10 0.1616 0.1091
> > 20 0.0735 0.0679
> > 30 0.0775 0.0705
> > 40 0.1097 0.1189
> > 50 0.1471 0.1436
> > 60 0.0468 0.048
> > 70 0.0667 0.0652
> > 80 0.0727 0.086
> > 90 0.0664 0.0707
> > 100 0.1336 0.114
> > 110 0.0899 0.0841
> > 120 0.0572 0.0598
> > 130 0.0506 0.0482
> > 140 0.0723 0.0767
> > 150 0.1466 0.1439
> > 160 0.0703 0.0601
> > 170 0.081 0.0853
> > 180 0.0278 0.027
> > 190 0.1121 0.1024
> > 200 0.3136 0.2981
> >
> >
> > 2013/3/28 Dr. Vitaly Chaban 
> > >
> > > >
> > > > if I do as you said, I will get only one diffusion coefficient. I
> want
> > to
> > > > calculate one diffusion coefficient for each 10
> > > > ns of the simulation time of 200 ns. That is, I want to get 20
> > diffusion
> > > > values.
> > > >
> > > > 2013/3/28 David van der Spoel 
> > > >
> > > >> On 2013-03-28 10:40, Ahmet yıldırım wrote:
> > > >>
> > > >>> Dear users,
> > > >>>
> > > >>> This time, I calculated the diffusion coefficients of protein for
> > each 10
> > > >>> ns of the simulation providing a total simulation time of 200 ns.
> > > >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit
> -1
> > > >>> -endfit -1 -b 0 -e 1
> > > >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit
> -1
> > > >>> -endfit -1 -b 10001 -e 2
> > > >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit
> -1
> > > >>> -endfit -1 -b 20001 -e 3
> > > >>> 
> > > >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit
> -1
> > > >>> -endfit -1 -b 190001 -e 20
> > > >>>
> > > >>
> > > >> Set trestart to 10001 (no restarts), or do one run with
> > > >>
> > > >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
> > > >>
> > >
> > >
> > > I believe the advice was to increase "trestart" and you can decide
> > > yourself how much to increase.
> > >
> > > Most likely, your protein deserves better sampling than 10 ns for a
> > > linear diffusion.
> > >
> > > Dr. Vitaly Chaban
> > > --
> > > 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
> >
>
>
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ==

[gmx-users] Freezing group

[Алексей Раевский]

Hi dear All!
Good day dear forum! I have a question abour freezing of atoms during MD.
The idea is that - I have a protein and one domain contains a site. Also I
have two ligands, one of them is better inhibitor in comparison with
another one. To prepare the topology of the inhibitor I need to use a
R.E.D.III server. As there are several different fitting methods, so I have
to carry out a series of short MDs (about 5-10 ns) for each of them. The
question is - is it possible to isolate this domain and fix/freeze last
residues of the hairpin/linker to prevent movement of domain segments? I
know that this is not the way to study ligand-protein interaction, however
I just want to use it for understanding which topology generation method is
better.
Thank you!

-- 

*

Nemo me impune lacessit*
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[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-- 
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Re: [gmx-users] TOP file question

[Peter Eastman]

Hi Justin,

So if I understand you correctly, there are actually three different ways the 
parameters can be specified.  In order of decreasing precedence:

1. If there's a [pairs] line and it includes parameters, use those parameters.

2. If there's a [pairs] line and it doesn't include parameters, look for a 
corresponding [pairtypes] lines and, if we find one, use that.

3. If gen-pairs is "yes", then generate parameters for all 1-2, 1-3, and 1-4 
pairs for which we did not already find parameters in step 1 or 2 (regardless 
of whether or not a [pairs] line exists for a particular pair).

Is that correct?

Thanks!

Peter


On Mar 28, 2013, at 4:20 AM, Justin Lemkul  wrote:

> 
> 
> On 3/27/13 5:12 PM, Peter Eastman wrote:
>> I'm implementing a TOP file reader, and I have a question about an ambiguity 
>> in the format.  The [ pairs ] block lists atom pairs that should be handled 
>> specially (exclusions and 1-4 interactions).  In addition, the gen-pairs 
>> flag can indicate that pairs are generated automatically.  But all the files 
>> I've looked at include BOTH of these things, and I'm not sure how to 
>> interpret that.
>> 
>> Can I assume that all pairs generated by gen-pairs are already included in 
>> the list, or might I have to generate additional ones?
>> 
>> Can I assume that all pairs listed in the file where generated by gen-pairs, 
>> or might there be additional pairs that came from somewhere else?
>> 
>> What if the two definitions disagree with each other, and the [ pairs ] 
>> block lists different parameters for a pair than would be generated 
>> automatically?  Which should I use?
>> 
> 
> The presence of [pairs] is not dependent upon gen-pairs, but the parameters 
> utilized by those pairs are.  All force fields deal with 1-4 interactions in 
> some way, but the manner in which they do so is different.  For instance, in 
> Gromos96 parameter sets, the gen-pairs keyword is set to "no," and all pair 
> interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, 
> whereas for other force fields (OPLS, AMBER), the pair interactions are 
> simply calculated according to normal combination rules with fudge factors 
> (i.e., gen-pairs set to "yes").  CHARMM uses a hybrid approach wherein some 
> pairs are set in [pairtypes], but anything not listed there is generated.
> 
> -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!
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[gmx-users] invalid pairstype 180

[Monoj Mon Kalita]

Dear GMX-Users

I have a problem while trying to insert a drug molecule into my simulation.
I have the topology file generated from the ATB-server. And accordingly I
have edited the aminoacid.rtp & ffbonded.itp file. I have transcribed the
forcefield parameters into GROMOS96 format. here is my .itp file for that
molecule. My problem is that after doing all the things when i tried to do
sd minimization then i got the error message like

*Program grompp, VERSION 4.5.5*
*Source code file:
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/topdirs.c, line: 107*
*
*
*Fatal error:*
*Invalid pairs type 180*
*For more information and tips for troubleshooting, please check the GROMACS
*
*website at http://www.gromacs.org/Documentation/Errors*

What may be the reason ? And when i studied through the .itp file then i
have found the 1-4 interactions in the [ pairs ] section followed by the
excluded 1-4 interactions. Now, my other question is that should I address
these 1-4 interactions in the ffnonbonded.itp file ! Looking forward for
kind response.

[ moleculetype ]
; Name   nrexcl
_NW5 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1   CH31_NW5C141   -0.000  15.0350  ;  0.000
2 C1_NW5 C82   -0.217  12.0110
3HC1_NW5 H120.138   1.0080
4 C1_NW5C112   -0.111  12.0110
5 C1_NW5C1520.717  12.0110
6 O1_NW5 O12   -0.580  15.9994
7 N1_NW5 N22   -0.663  14.0067
8 H1_NW5 H820.372   1.0080
9 C1_NW5C1620.785  12.0110
   10NT1_NW5 N52   -0.939  14.0067
   11 H1_NW5 H920.398   1.0080
   12 H1_NW5H1020.398   1.0080
   13NR1_NW5 N12   -0.841  14.0067
   14 H1_NW5 H720.347   1.0080
   15 C1_NW5 C120.040  12.0110
   16 C1_NW5 C220.040  12.0110
   17 C1_NW5 C32   -0.151  12.0110
   18 C1_NW5 C520.150  12.0110
   19 C1_NW5C1320.149  12.0110
   20HC1_NW5H1420.099   1.0080
   21NR1_NW5 N32   -0.567  14.0067
   22NR1_NW5 N420.436  14.0067  ;  0.000
   23 C1_NW5C103   -0.154  12.0110
   24HC1_NW5 H630.154   1.0080  ;  0.000
   25 C1_NW5 C64   -0.154  12.0110
   26HC1_NW5 H340.154   1.0080  ;  0.000
   27 C1_NW5 C45   -0.154  12.0110
   28HC1_NW5 H250.154   1.0080  ;  0.000
   29 C1_NW5 C96   -0.152  12.0110
   30HC1_NW5 H560.152   1.0080  ;  0.000
   31 C1_NW5 C77   -0.154  12.0110
   32HC1_NW5 H470.154   1.0080  ;  0.000
   33 C1_NW5C128   -0.200  12.0110
   34HC1_NW5H1580.200   1.0080  ;  0.000
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
1   222   0.1470   8.7100e+06
232   0.1090   1.2300e+07
242   0.1390   8.6600e+06
2   182   0.1435   6.1000e+06
452   0.1520   5.4300e+06
4   232   0.1435   6.1000e+06
562   0.1230   1.6600e+07
572   0.1380   1.1000e+07
782   0.1000   1.8700e+07
792   0.1400   8.5400e+06
9   102   0.1400   8.5400e+06
9   132   0.1320   1.2000e+07
   10   112   0.1000   1.8700e+07
   10   122   0.1000   1.8700e+07
   13   142   0.1000   1.8700e+07
   15   162   0.1435   6.1000e+06
   15   172   0.1480   5.7300e+06
   15   272   0.1390   8.6600e+06
   16   182   0.1435   6.1000e+06
   16   252   0.1435   6.1000e+06
   17   192   0.1390   8.6600e+06
   17   332   0.1390   8.6600e+06
   18   312   0.1435   6.1000e+06
   19   202   0.1090   1.2300e+07
   19   212   0.1330   1.0600e+07
   21   222   0.1360   4.7700e+06
   22   332   0.1350   1.0300e+07
   23   242   0.1090   1.2300e+07
   23   252   0.1390   1.0800e+07
   25   262   0.1090   1.2300e+07
   27   282   0.1090   1.2300e+07
   27   292   0.1435   6.1000e+06
   29   302   0.1090   1.2300e+07
   29   312   0.1390   1.0800e+07
   31   322   0.1090   1.2300e+07
   33   342   0.1090   1.2300e+07
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
261
271
481
491
5   101
5   131
681
691
6   231
7   111
7   121
7   141
7   231
8   101
8   131
   10   141
   11   131
   12   131
   16   19

Re: [gmx-users] Re: diffusion constant level off

[Justin Lemkul]

On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım  wrote:

> Dear users,
>
> Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
> is there a bug with g_msd?
>
>
I see no evidence for a bug, and you should avoid such speculation unless
you know exactly how the program should behave. Only then, after an
analysis of known quantities or behavior, can we discuss bugginess. Do you
know how g_msd works? Do you know what all of the flags are doing, or are
you just making adjustments hoping for clarity? You may find the following
post very illuminating:

http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html

-Justin


> Commands for trestart to 20 ps:
> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
> -endfit -1 -b 0 -e 1
> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
> -endfit -1 -b 1 -e 2
> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
> -endfit -1 -b 2 -e 3
> ...
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> -endfit -1 -b 19 -e 20
>
> Commands for trestart to 1000 ps:
> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 0 -e 1
> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 1 -e 2
> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 2 -e 3
> ...
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 19 -e 20
>
>
> D1 (cm^2/s):Diffusion for trestart to 20 ps
> D2 (cm^2/s):Diffusion for trestart to 1000 ps
> Time (ns) D1 D2
> 10 0.1616 0.1091
> 20 0.0735 0.0679
> 30 0.0775 0.0705
> 40 0.1097 0.1189
> 50 0.1471 0.1436
> 60 0.0468 0.048
> 70 0.0667 0.0652
> 80 0.0727 0.086
> 90 0.0664 0.0707
> 100 0.1336 0.114
> 110 0.0899 0.0841
> 120 0.0572 0.0598
> 130 0.0506 0.0482
> 140 0.0723 0.0767
> 150 0.1466 0.1439
> 160 0.0703 0.0601
> 170 0.081 0.0853
> 180 0.0278 0.027
> 190 0.1121 0.1024
> 200 0.3136 0.2981
>
>
> 2013/3/28 Dr. Vitaly Chaban 
> >
> > >
> > > if I do as you said, I will get only one diffusion coefficient. I want
> to
> > > calculate one diffusion coefficient for each 10
> > > ns of the simulation time of 200 ns. That is, I want to get 20
> diffusion
> > > values.
> > >
> > > 2013/3/28 David van der Spoel 
> > >
> > >> On 2013-03-28 10:40, Ahmet yıldırım wrote:
> > >>
> > >>> Dear users,
> > >>>
> > >>> This time, I calculated the diffusion coefficients of protein for
> each 10
> > >>> ns of the simulation providing a total simulation time of 200 ns.
> > >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
> > >>> -endfit -1 -b 0 -e 1
> > >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
> > >>> -endfit -1 -b 10001 -e 2
> > >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
> > >>> -endfit -1 -b 20001 -e 3
> > >>> 
> > >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> > >>> -endfit -1 -b 190001 -e 20
> > >>>
> > >>
> > >> Set trestart to 10001 (no restarts), or do one run with
> > >>
> > >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
> > >>
> >
> >
> > I believe the advice was to increase "trestart" and you can decide
> > yourself how much to increase.
> >
> > Most likely, your protein deserves better sampling than 10 ns for a
> > linear diffusion.
> >
> > Dr. Vitaly Chaban
> > --
> > 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!
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>



-- 



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


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Re: [gmx-users] Re: diffusion constant level off

[Dr. Vitaly Chaban]

perhaps, you could make a plot??

it is difficult to understand what you are speaking about.

Dr. Vitaly Chaban




On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım  wrote:
> Dear users,
>
> Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is
> there a bug with g_msd?
>
> Commands for trestart to 20 ps:
> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit
> -1 -b 0 -e 1
> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit
> -1 -b 1 -e 2
> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit
> -1 -b 2 -e 3
> ...
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> -endfit -1 -b 19 -e 20
>
> Commands for trestart to 1000 ps:
> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 0 -e 1
> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 1 -e 2
> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 2 -e 3
> ...
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 19 -e 20
>
>
> D1 (cm^2/s):Diffusion for trestart to 20 ps
> D2 (cm^2/s):Diffusion for trestart to 1000 ps
> Time (ns) D1 D2
> 10 0.1616 0.1091
> 20 0.0735 0.0679
> 30 0.0775 0.0705
> 40 0.1097 0.1189
> 50 0.1471 0.1436
> 60 0.0468 0.048
> 70 0.0667 0.0652
> 80 0.0727 0.086
> 90 0.0664 0.0707
> 100 0.1336 0.114
> 110 0.0899 0.0841
> 120 0.0572 0.0598
> 130 0.0506 0.0482
> 140 0.0723 0.0767
> 150 0.1466 0.1439
> 160 0.0703 0.0601
> 170 0.081 0.0853
> 180 0.0278 0.027
> 190 0.1121 0.1024
> 200 0.3136 0.2981
>
>
> 2013/3/28 Dr. Vitaly Chaban 
>>
>> >
>> > if I do as you said, I will get only one diffusion coefficient. I want
>> > to
>> > calculate one diffusion coefficient for each 10
>> > ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
>> > values.
>> >
>> > 2013/3/28 David van der Spoel 
>> >
>> >> On 2013-03-28 10:40, Ahmet yıldırım wrote:
>> >>
>> >>> Dear users,
>> >>>
>> >>> This time, I calculated the diffusion coefficients of protein for each
>> >>> 10
>> >>> ns of the simulation providing a total simulation time of 200 ns.
>> >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
>> >>> -endfit -1 -b 0 -e 1
>> >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
>> >>> -endfit -1 -b 10001 -e 2
>> >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
>> >>> -endfit -1 -b 20001 -e 3
>> >>> 
>> >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
>> >>> -endfit -1 -b 190001 -e 20
>> >>>
>> >>
>> >> Set trestart to 10001 (no restarts), or do one run with
>> >>
>> >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
>> >>
>>
>>
>> I believe the advice was to increase "trestart" and you can decide
>> yourself how much to increase.
>>
>> Most likely, your protein deserves better sampling than 10 ns for a
>> linear diffusion.
>>
>> Dr. Vitaly Chaban
>> --
>> 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
--
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Re: [gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

Dear users,

Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?

Commands for trestart to 20 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
-endfit -1 -b 1 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
-endfit -1 -b 2 -e 3
...
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
-endfit -1 -b 19 -e 20

Commands for trestart to 1000 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 1 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 2 -e 3
...
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 19 -e 20


D1 (cm^2/s):Diffusion for trestart to 20 ps
D2 (cm^2/s):Diffusion for trestart to 1000 ps
Time (ns) D1 D2
10 0.1616 0.1091
20 0.0735 0.0679
30 0.0775 0.0705
40 0.1097 0.1189
50 0.1471 0.1436
60 0.0468 0.048
70 0.0667 0.0652
80 0.0727 0.086
90 0.0664 0.0707
100 0.1336 0.114
110 0.0899 0.0841
120 0.0572 0.0598
130 0.0506 0.0482
140 0.0723 0.0767
150 0.1466 0.1439
160 0.0703 0.0601
170 0.081 0.0853
180 0.0278 0.027
190 0.1121 0.1024
200 0.3136 0.2981


2013/3/28 Dr. Vitaly Chaban 
>
> >
> > if I do as you said, I will get only one diffusion coefficient. I want
to
> > calculate one diffusion coefficient for each 10
> > ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
> > values.
> >
> > 2013/3/28 David van der Spoel 
> >
> >> On 2013-03-28 10:40, Ahmet yıldırım wrote:
> >>
> >>> Dear users,
> >>>
> >>> This time, I calculated the diffusion coefficients of protein for
each 10
> >>> ns of the simulation providing a total simulation time of 200 ns.
> >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
> >>> -endfit -1 -b 0 -e 1
> >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
> >>> -endfit -1 -b 10001 -e 2
> >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
> >>> -endfit -1 -b 20001 -e 3
> >>> 
> >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> >>> -endfit -1 -b 190001 -e 20
> >>>
> >>
> >> Set trestart to 10001 (no restarts), or do one run with
> >>
> >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
> >>
>
>
> I believe the advice was to increase "trestart" and you can decide
> yourself how much to increase.
>
> Most likely, your protein deserves better sampling than 10 ns for a
> linear diffusion.
>
> Dr. Vitaly Chaban
> --
> 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
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Re: [gmx-users] retraining multiple protein ligand interactions using pull-code

[Justin Lemkul]

On Thu, Mar 28, 2013 at 8:18 AM, Saravanan  wrote:

> Thank you.. I hoped it would be simpler. how do I go about creating unified
> protein-ligand [moleculartype] directives. Can you suggest any material
> available on this topic? that would be extremely helpful.
>
>
Depending on the complexity of the ligand, you may be able to do it by hand
by simply adding the ligand parameters after the protein in all relevant
directives of the Protein [moleculetype]. Otherwise, you will need to
create an .rtp entry for the ligand and use pdb2gmx command line options to
create the merged topologies (using, e.g. chain identifiers to indicate
that they should be placed in the same [moleculetype] directive). In this
case, refer to
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
.

This is a rather advanced topic, so do as much tutorial material and other
simulations as you can to familiarize yourself with a "standard" Gromacs
workflow. You should also read Chapter 5 of the manual thoroughly to
understand topology organization.

-Justin

-- 



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


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Re: [gmx-users] retraining multiple protein ligand interactions using pull-code

[Saravanan]

Thank you.. I hoped it would be simpler. how do I go about creating unified
protein-ligand [moleculartype] directives. Can you suggest any material
available on this topic? that would be extremely helpful.

-Saravanan


On 28 March 2013 16:45, Justin Lemkul  wrote:

>
>
> On 3/28/13 4:01 AM, Saravanan wrote:
>
>> Hello everyone,
>>
>> I am new to using gromacs. I am currently studying an enzyme catalysing a
>> transfer reaction. there are two substrates and I want to restraint
>> specific interactions between different parts of the ligands and the
>> protein. As I understand so far from reading various discussions in the
>> group, restraining such interactions is possible through pull code, But we
>> can assign only one pull group0, I am wondering if there is better way to
>> restraint multiple interactions between multiple molecules in a single
>> simulation. If not through pull-code, what will be the best way to ensure
>> many specific intermolecular restraints?
>>
>>
> Use distance restraints.  Unfortunately, this will require a lot of
> topology hacking to create unified protein-ligand [moleculetype]
> directives.  Restraints (like any bonded interaction) can only be applied
> within a [moleculetype], not between 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
>
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[gmx-users] Re: diffusion constant level off

[Dr. Vitaly Chaban]

>
> if I do as you said, I will get only one diffusion coefficient. I want to
> calculate one diffusion coefficient for each 10
> ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
> values.
>
> 2013/3/28 David van der Spoel 
>
>> On 2013-03-28 10:40, Ahmet yıldırım wrote:
>>
>>> Dear users,
>>>
>>> This time, I calculated the diffusion coefficients of protein for each 10
>>> ns of the simulation providing a total simulation time of 200 ns.
>>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
>>> -endfit -1 -b 0 -e 1
>>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
>>> -endfit -1 -b 10001 -e 2
>>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
>>> -endfit -1 -b 20001 -e 3
>>> 
>>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
>>> -endfit -1 -b 190001 -e 20
>>>
>>
>> Set trestart to 10001 (no restarts), or do one run with
>>
>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
>>


I believe the advice was to increase "trestart" and you can decide
yourself how much to increase.

Most likely, your protein deserves better sampling than 10 ns for a
linear diffusion.

Dr. Vitaly Chaban
--
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Re: [gmx-users] TOP file question

[Justin Lemkul]

On 3/27/13 5:12 PM, Peter Eastman wrote:

I'm implementing a TOP file reader, and I have a question about an ambiguity in 
the format.  The [ pairs ] block lists atom pairs that should be handled 
specially (exclusions and 1-4 interactions).  In addition, the gen-pairs flag 
can indicate that pairs are generated automatically.  But all the files I've 
looked at include BOTH of these things, and I'm not sure how to interpret that.

Can I assume that all pairs generated by gen-pairs are already included in the 
list, or might I have to generate additional ones?

Can I assume that all pairs listed in the file where generated by gen-pairs, or 
might there be additional pairs that came from somewhere else?

What if the two definitions disagree with each other, and the [ pairs ] block 
lists different parameters for a pair than would be generated automatically?  
Which should I use?



The presence of [pairs] is not dependent upon gen-pairs, but the parameters 
utilized by those pairs are.  All force fields deal with 1-4 interactions in 
some way, but the manner in which they do so is different.  For instance, in 
Gromos96 parameter sets, the gen-pairs keyword is set to "no," and all pair 
interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, 
whereas for other force fields (OPLS, AMBER), the pair interactions are simply 
calculated according to normal combination rules with fudge factors (i.e., 
gen-pairs set to "yes").  CHARMM uses a hybrid approach wherein some pairs are 
set in [pairtypes], but anything not listed there is generated.


-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


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Re: [gmx-users] retraining multiple protein ligand interactions using pull-code

[Justin Lemkul]

On 3/28/13 4:01 AM, Saravanan wrote:

Hello everyone,

I am new to using gromacs. I am currently studying an enzyme catalysing a
transfer reaction. there are two substrates and I want to restraint
specific interactions between different parts of the ligands and the
protein. As I understand so far from reading various discussions in the
group, restraining such interactions is possible through pull code, But we
can assign only one pull group0, I am wondering if there is better way to
restraint multiple interactions between multiple molecules in a single
simulation. If not through pull-code, what will be the best way to ensure
many specific intermolecular restraints?



Use distance restraints.  Unfortunately, this will require a lot of topology 
hacking to create unified protein-ligand [moleculetype] directives.  Restraints 
(like any bonded interaction) can only be applied within a [moleculetype], not 
between 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


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Re: [gmx-users] bond conversion between charmm and g96

[Justin Lemkul]

On 3/28/13 5:18 AM, 라지브간디 wrote:


p{margin:0;padding:0;}


Dear Justin,


Thank for your pointing out my issues. I just want to know how it can be 
converted.


I have referred the equation in chapter 4 and do not know exactly how I use 
them.


For example, The C-O bond distance and force constant written as (0.112  and 
3.7000e+07 ) in gromos, whereas  in charmm27 written as ( 0.1128 and 933032.0).


I found the equation for g96 type covalent potential Vb (rij) and force 
constant Fi(rij) and don't know how do i use this for above purpose?


Could you elaborate an example how it can be done? Thanks a lot.



Different force fields handle bonds in different ways.  Gromos96 uses a quartic 
bond potential (equation 4.36 in the manual), while CHARMM uses a normal 
harmonic potential (equation 4.34).  The data in ffbonded.itp are thus 
interpreted differently, and in fact, when using a Gromos96 force field, the 
square root of bond lengths are used, etc.  If you multiply the CHARMM force 
constant by 4, you arrive at the Gromos96 force constant (more or less).  Note 
that force constants are irrelevant if using constraints on these bonds.


-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


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Re: [gmx-users] Re: Atoms are fused after inserting in membrane

[Justin Lemkul]

On 3/27/13 11:32 PM, sdshine wrote:

Dear all,

Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that, can I proceed as such with my system, since there
is no problem in grompp and EM step (except high energy on some atom).

or Do I need to manually remove those overlapping lipids and water
molecules.



No, InflateGRO does this for you.  After inflation, there should be no water in 
the system and the lipids should have expanded outward.  Any that were too close 
(as defined by the cutoff specified on the command line) should have been deleted.


-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


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Re: [gmx-users] Re: Atoms are fused after inserting in membrane

[Justin Lemkul]

On 3/28/13 6:38 AM, Dr. Vitaly Chaban wrote:

Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that, can I proceed as such with my system, since there
is no problem in grompp and EM step (except high energy on some atom).



The energy will normalize during molecular dynamics stage.



...assuming the energy is not so high as to cause an immediate crash :)

-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


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Re: [gmx-users] no CUDA-capable device is detected

[Chandan Choudhury]

Hi !!

I problem with the permission of /dev/nvidia*

changed it to 0666 /dev/nvidia*

Everything resolved. mdrun  can be executed as normal user.

Thanks everyone.

Chandan




--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury wrote:

>
> On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll wrote:
>
>> Hi,
>>
>> If mdrun says that it could not detect GPUs it simply means that the GPU
>> enumeration found no GPUs, otherwise it would have printed what was found.
>> This is rather strange because mdrun uses the same mechanism the
>> deviceQuery SDK example. I really don't have a good idea what could be the
>> issue, but you could try recompiling or compiling with CUDA 4.2 to see if
>> any of that makes a difference.
>>
>> Let us know if you figured out something.
>>
>> Cheers,
>>
>
> Thanks Szilárd for the eye opening comment.
>
> I just tried running gromacs as root. I recalled I had executed
> deviceQuery as root. While executing as user it produces the same error :
>
> */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery
> Starting...
>
>  CUDA Device Query (Runtime API) version (CUDART static linking)
>
> cudaGetDeviceCount returned 38
> -> no CUDA-capable device is detected*
>
> Now, running gromacs as root, it is running successfully (I suppose).
>
> Output of nvidia-smi
>
>
> +--+
>
> | NVIDIA-SMI 4.310.40   Driver Version: 310.40
> |
>
> |---+--+--+
> | GPU  Name | Bus-IdDisp.  | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
> M. |
>
> |===+==+==|
> |   0  NVS 300  | :03:00.0 N/A |
> N/A |
> | N/A   48C  N/A N/A /  N/A |   3%   17MB /  511MB | N/A
> Default |
>
>
> +---+--+--+
> |   1  Tesla K20c   | :04:00.0 Off |
> Off |
> | 50%   62CP0   106W / 225W |   2%   87MB / 5119MB | 76%
> Default |
>
>
> +---+--+--+
>
>
>
> +-+
> | Compute processes:   GPU
> Memory |
> |  GPU   PID  Process name
> Usage  |
>
> |=|
> |0Not
> Supported   |
> |1  9127  mdrun_461
> 72MB  |
>
> +-+
>
> Output of md.log
>
> 2 GPUs detected:
>   #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC:  no, stat: compatible
>   #1: NVIDIA NVS 300, compute cap.: 1.2, ECC:  no, stat: incompatible
>
> 1 GPU auto-selected for this run: #0
>
>
> I think there is something relate to permissions. Though nvcc has 755
> permission, something else might require additional permissions.
>
> Chandan
>
>
>> --
>> Szilárd
>>
>>
>> On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess  wrote:
>>
>> >
>> > Hi,
>> >
>> > I am not the expert on GPU detection, so we'll need to wait until an
>> > expert replies.
>> > Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
>> > mdrun -ntmpi 1 -gpu_id 0
>> >
>> > Also your tpr file is from an older version. It will not run on a GPU.
>> > You need to set the mdp option:
>> > cutoff-scheme = Verlet
>> > and run grompp to get a new tpr file.
>> >
>> > Cheers,
>> >
>> > Berk
>> >
>> > > From: iitd...@gmail.com
>> > > Date: Thu, 28 Mar 2013 14:57:16 +0530
>> > > Subject: Re: [gmx-users] no CUDA-capable device is detected
>> > > To: gmx-users@gromacs.org
>> > >
>> > > On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess  wrote:
>> > >
>> > > >
>> > > > Hi,
>> > > >
>> > > > The code compiled, so the compiler is not the issue.
>> > > >
>> > > > I guess mdrun picked up GPU 0, which it should have ignored. You
>> only
>> > want
>> > > > to use GPU 1.
>> > > >
>> > > > Could you try running:
>> > > > mdrun -ntmpi 1 -gpu_id 1
>> > > >
>> > >
>> > > $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr
>> > > Note: file tpx version 73, software tpx version 83
>> > >
>> > > NOTE: Error occurred during GPU detection:
>> > >   no CUDA-capable device is detected
>> > >   Can not use GPU acceleration, will fall back to CPU kernels.
>> > >
>> > >
>> > > No GPUs detected
>> > >
>> > >
>> > > ---
>> > > Program mdrun_461, VERSION 4.6.1
>> > > Source code file:
>> > > /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line:
>> > 580
>> > >
>> > > Fatal error:
>> > > Some of the requested GPUs do not exist, behave strangely, or are not
>> > > compatible:
>> > > GPU #1: inexistent
>> > >
>> > > >
>> > > > Cheers,
>> > > >
>> >

Re: [gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

Dear Prof.Spoel,

if I do as you said, I will get only one diffusion coefficient. I want to
calculate one diffusion coefficient for each 10
ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
values.

2013/3/28 David van der Spoel 

> On 2013-03-28 10:40, Ahmet yıldırım wrote:
>
>> Dear users,
>>
>> This time, I calculated the diffusion coefficients of protein for each 10
>> ns of the simulation providing a total simulation time of 200 ns.
>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 0 -e 1
>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 10001 -e 2
>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 20001 -e 3
>> 
>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 190001 -e 20
>>
>
> Set trestart to 10001 (no restarts), or do one run with
>
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
>
>
>
>> I have strange Diffusion results (especially 10,50,100,150,200 ns). How
>> can
>> I fix this problem?
>> Results:
>> Time (ns) D(cm^2/s)
>> 10 0.1616
>> 20 0.0735
>> 30 0.0775
>> 40 0.1097
>> 50 0.1471
>> 60 0.0468
>> 70 0.0667
>> 80 0.0727
>> 90 0.0664
>> 100 0.1336
>> 110 0.0899
>> 120 0.0572
>> 130 0.0506
>> 140 0.0723
>> 150 0.1466
>> 160 0.0703
>> 170 0.081
>> 180 0.0278
>> 190 0.1121
>> 200 0.3136
>>
>>
>>
>> 2013/3/27 Ahmet yıldırım 
>>
>>>
>>> Dear users,
>>>
>>> I used the following commands to get diffusion constants (every 10 ns) of
>>>
>> a simulation of 100 ns . The number of frame is 5001 (write .xtc
>> trajectory
>> every 20 ps).  I looked at RMSD vs average structure, RMSD vs starting
>> structure, Radius of gyration, RMSD matrix. This simulation has reached to
>> converge at last 50 ns.
>>
>>> g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1
>>> g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2
>>> g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3
>>> ...
>>> g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10
>>>
>>> 1.) I used the above commands without the following flags ( -type,
>>>
>> -lateral and -ten). Which diffusion will the above comands give? is it
>> bulk
>> diffusion?
>>
>>> Gromacs manual:
>>> -type:Compute diffusion coefficient in one direction:no, x, y or z
>>> -lateral:Calculate the lateral diffusion in a plane perpendicular to: no,
>>>
>> x, y or z
>>
>>> -ten:Calculate the full tensor
>>> 2.) I plotted diffusions (10 values) as function of time. Diffusions dont
>>>
>> converge. Did I do any steps by mistake?
>>
>>> 3.) From manual:
>>> The diffusion constant is calculated by least squares fitting a straight
>>>
>> line (D*t + c)...
>>
>>> What is (D*t + c)? What are the meaning of D and c?
>>> 4.) What should be "Time between restarting points in trajectory"?
>>>
>>> Thanks in advance
>>> --
>>> Ahmet Yıldırım
>>>
>>
>>
>>
>>
>> --
>> Ahmet Yıldırım
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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
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Re: [gmx-users] no CUDA-capable device is detected

[Chandan Choudhury]

On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll wrote:

> Hi,
>
> If mdrun says that it could not detect GPUs it simply means that the GPU
> enumeration found no GPUs, otherwise it would have printed what was found.
> This is rather strange because mdrun uses the same mechanism the
> deviceQuery SDK example. I really don't have a good idea what could be the
> issue, but you could try recompiling or compiling with CUDA 4.2 to see if
> any of that makes a difference.
>
> Let us know if you figured out something.
>
> Cheers,
>

Thanks Szilárd for the eye opening comment.

I just tried running gromacs as root. I recalled I had executed deviceQuery
as root. While executing as user it produces the same error :

*/root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery
Starting...

 CUDA Device Query (Runtime API) version (CUDART static linking)

cudaGetDeviceCount returned 38
-> no CUDA-capable device is detected*

Now, running gromacs as root, it is running successfully (I suppose).

Output of nvidia-smi

+--+

| NVIDIA-SMI 4.310.40   Driver Version: 310.40
|
|---+--+--+
| GPU  Name | Bus-IdDisp.  | Volatile Uncorr.
ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
M. |
|===+==+==|
|   0  NVS 300  | :03:00.0 N/A |
N/A |
| N/A   48C  N/A N/A /  N/A |   3%   17MB /  511MB | N/A
Default |
+---+--+--+
|   1  Tesla K20c   | :04:00.0 Off |
Off |
| 50%   62CP0   106W / 225W |   2%   87MB / 5119MB | 76%
Default |
+---+--+--+


+-+
| Compute processes:   GPU
Memory |
|  GPU   PID  Process name
Usage  |
|=|
|0Not
Supported   |
|1  9127  mdrun_461
72MB  |
+-+

Output of md.log

2 GPUs detected:
  #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC:  no, stat: compatible
  #1: NVIDIA NVS 300, compute cap.: 1.2, ECC:  no, stat: incompatible

1 GPU auto-selected for this run: #0


I think there is something relate to permissions. Though nvcc has 755
permission, something else might require additional permissions.

Chandan


> --
> Szilárd
>
>
> On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess  wrote:
>
> >
> > Hi,
> >
> > I am not the expert on GPU detection, so we'll need to wait until an
> > expert replies.
> > Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
> > mdrun -ntmpi 1 -gpu_id 0
> >
> > Also your tpr file is from an older version. It will not run on a GPU.
> > You need to set the mdp option:
> > cutoff-scheme = Verlet
> > and run grompp to get a new tpr file.
> >
> > Cheers,
> >
> > Berk
> >
> > > From: iitd...@gmail.com
> > > Date: Thu, 28 Mar 2013 14:57:16 +0530
> > > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > > To: gmx-users@gromacs.org
> > >
> > > On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess  wrote:
> > >
> > > >
> > > > Hi,
> > > >
> > > > The code compiled, so the compiler is not the issue.
> > > >
> > > > I guess mdrun picked up GPU 0, which it should have ignored. You only
> > want
> > > > to use GPU 1.
> > > >
> > > > Could you try running:
> > > > mdrun -ntmpi 1 -gpu_id 1
> > > >
> > >
> > > $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr
> > > Note: file tpx version 73, software tpx version 83
> > >
> > > NOTE: Error occurred during GPU detection:
> > >   no CUDA-capable device is detected
> > >   Can not use GPU acceleration, will fall back to CPU kernels.
> > >
> > >
> > > No GPUs detected
> > >
> > >
> > > ---
> > > Program mdrun_461, VERSION 4.6.1
> > > Source code file:
> > > /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line:
> > 580
> > >
> > > Fatal error:
> > > Some of the requested GPUs do not exist, behave strangely, or are not
> > > compatible:
> > > GPU #1: inexistent
> > >
> > > >
> > > > Cheers,
> > > >
> > > > berk
> > > >
> > > > > Date: Thu, 28 Mar 2013 10:51:58 +0200
> > > > > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > > > > From: g...@bioacademy.gr
> > > > > To: gmx-users@gromacs.org
> > > > >
> > > > > Hi Chandan
> > > > >
> > > > > Are you using the same version of GCC compiler that you used to
> > compile
> > > > > CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I
> think
> > > > there
> > > > > was some kind of incompatibility between the two).
> > > >
> > >
> >

[gmx-users] SMD : pulling both primes of DNA

[Thomas Schlesier]

The easiest solution would be using 'pull_geometry = distance' in all 
three dimensions. Then you can be sure that both groups are pulled 
together. Small remark: One group would be fixed for the pulling, and 
the second group gets pulled towards the first group. So if you want to 
have both groups really close, this setup would be the easiest solution.


If you really to pull both groups to a point in the middle between them, 
i think you would need 'pull_geometry = position':
Use some part of the DNA as the reference group and put the origin of 
the pulling  (via 'pull_init') to the middle point. Then make two 
pull-groups + 'pull_vec1' or 'pull_vec2', from each DNA part, which you 
want to pull to the middle point.
In principle this setup should work, but you can run into problems if 
the structure of the DNA changes and the middle point, to where you pull 
both groups, moves somewhat around.

hard to explain...

I would stick to the first approach...
What pull-mode did you use? You could use 'pull = constraint', measure 
the distance between both groups and then pull with a given pulling 
velocity so long till both groups should meet. Since you use a 
constraint instead of a restraining potential, the groups should be 
definitly pulled together (or some other parameters in the .mdp file are 
wrong).


Greetings
Thomas






Am 27.03.2013 20:16, schrieb gmx-users-requ...@gromacs.org:

Hello All,

My simulation system is composed of DNA and want to pull both of the primes
at the same time towards each other.
I have tried every possible set of parameters in pull code...and i am not
able to pull them together.

it's like ...
the DNA molecule is aligned along Y-axis and if want to pull both ends at
the same time that means pulling in -Y and +Y direction at the same time.

if anyone successfully implemented such ...simulations... Please provide me
with some idea about this problem.

Thank you
Raghav


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Re: [gmx-users] no CUDA-capable device is detected

[Szilárd Páll]

Hi,

If mdrun says that it could not detect GPUs it simply means that the GPU
enumeration found no GPUs, otherwise it would have printed what was found.
This is rather strange because mdrun uses the same mechanism the
deviceQuery SDK example. I really don't have a good idea what could be the
issue, but you could try recompiling or compiling with CUDA 4.2 to see if
any of that makes a difference.

Let us know if you figured out something.

Cheers,

--
Szilárd


On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess  wrote:

>
> Hi,
>
> I am not the expert on GPU detection, so we'll need to wait until an
> expert replies.
> Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
> mdrun -ntmpi 1 -gpu_id 0
>
> Also your tpr file is from an older version. It will not run on a GPU.
> You need to set the mdp option:
> cutoff-scheme = Verlet
> and run grompp to get a new tpr file.
>
> Cheers,
>
> Berk
>
> > From: iitd...@gmail.com
> > Date: Thu, 28 Mar 2013 14:57:16 +0530
> > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > To: gmx-users@gromacs.org
> >
> > On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess  wrote:
> >
> > >
> > > Hi,
> > >
> > > The code compiled, so the compiler is not the issue.
> > >
> > > I guess mdrun picked up GPU 0, which it should have ignored. You only
> want
> > > to use GPU 1.
> > >
> > > Could you try running:
> > > mdrun -ntmpi 1 -gpu_id 1
> > >
> >
> > $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr
> > Note: file tpx version 73, software tpx version 83
> >
> > NOTE: Error occurred during GPU detection:
> >   no CUDA-capable device is detected
> >   Can not use GPU acceleration, will fall back to CPU kernels.
> >
> >
> > No GPUs detected
> >
> >
> > ---
> > Program mdrun_461, VERSION 4.6.1
> > Source code file:
> > /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line:
> 580
> >
> > Fatal error:
> > Some of the requested GPUs do not exist, behave strangely, or are not
> > compatible:
> > GPU #1: inexistent
> >
> > >
> > > Cheers,
> > >
> > > berk
> > >
> > > > Date: Thu, 28 Mar 2013 10:51:58 +0200
> > > > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > > > From: g...@bioacademy.gr
> > > > To: gmx-users@gromacs.org
> > > >
> > > > Hi Chandan
> > > >
> > > > Are you using the same version of GCC compiler that you used to
> compile
> > > > CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think
> > > there
> > > > was some kind of incompatibility between the two).
> > >
> >
> > There is an work around with gcc 4.7.2. Please see
> >
> http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html
> >
> > >
> > > > Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
> > > > worked in my system (MacOS/Darwin).
> > > >
> > > > Just make sure to set the variables CC and CXX to point to the right
> > > > compiler version when you run cmake.
> > > >
> > > > George
> > > >
> > > >
> > > > > Dear GMX Users,
> > > > >
> > > > > I am trying to execute Gromacs 4.6.1 on one of the GPU server:
> > > > > *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
> > > > > *gcc*: 4.7.2
> > > > >
> > > > > CUDA Library paths
> > > > > #CUDA-5.0
> > > > > export CUDA_HOME=/usr/local/cuda-5.0
> > > > > export PATH=$CUDA_HOME/bin:$PATH
> > > > > export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH
> > > > >
> > > > > The gromacs has been compiled with
> > > > >
> > > > > CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0
> > > cmake ..
> > > > > -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single
> > > > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461
> > > -DGMX_LIBS_SUFFIX=_461
> > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> > > > >
> > > > > *Error on executing mdrun
> > > > > *
> > > > > *
> > > > > *
> > > > > *NOTE: Error occurred during GPU detection:
> > > > > no CUDA-capable device is detected
> > > > > Can not use GPU acceleration, will fall back to CPU kernels.
> > > > >
> > > > >
> > > > > Will use 24 particle-particle and 8 PME only nodes
> > > > > This is a guess, check the performance at the end of the log file
> > > > > Using 32 MPI threads
> > > > >
> > > > > No GPUs detected
> > > > >
> > > > > *I checked my cuda installation. I am able to compile and execute
> the
> > > > > sample programmes e.g., deviceQuery.
> > > > >
> > > > > Also executed *nvidia-smi *:
> > > > > +--+
> > > > > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 |
> > > > >
> > >
> |---+--+--+
> > > > > | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
> > > > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> > > > >
> > >
> |===+==+==|
> > > > > | 0 NVS 300 | :03:00.0 N/A | N/A |
> > > > > | N/A 49C N/A N/A / N/A | 3% 1

[gmx-users] Re: Atoms are fused after inserting in membrane

[Dr. Vitaly Chaban]

> Does that mean the atoms will shrink and adjust at the time inflategro step
> and
> this closely packed lipids will stay apart? Because as you said the energy
> of course will be high on selected atoms during first EM step.
> Could you suggest me that, can I proceed as such with my system, since there
> is no problem in grompp and EM step (except high energy on some atom).


The energy will normalize during molecular dynamics stage.


Dr. Vitaly Chaban





> or Do I need to manually remove those overlapping lipids and water
> molecules.
>
> Thanks in advance
>
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Re: [gmx-users] Re: diffusion constant level off

[David van der Spoel]

On 2013-03-28 10:40, Ahmet yıldırım wrote:

Dear users,

This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
-endfit -1 -b 10001 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
-endfit -1 -b 20001 -e 3

g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
-endfit -1 -b 190001 -e 20


Set trestart to 10001 (no restarts), or do one run with

g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1



I have strange Diffusion results (especially 10,50,100,150,200 ns). How can
I fix this problem?
Results:
Time (ns) D(cm^2/s)
10 0.1616
20 0.0735
30 0.0775
40 0.1097
50 0.1471
60 0.0468
70 0.0667
80 0.0727
90 0.0664
100 0.1336
110 0.0899
120 0.0572
130 0.0506
140 0.0723
150 0.1466
160 0.0703
170 0.081
180 0.0278
190 0.1121
200 0.3136



2013/3/27 Ahmet yıldırım 


Dear users,

I used the following commands to get diffusion constants (every 10 ns) of

a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory
every 20 ps).  I looked at RMSD vs average structure, RMSD vs starting
structure, Radius of gyration, RMSD matrix. This simulation has reached to
converge at last 50 ns.

g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1
g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2
g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3
...
g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10

1.) I used the above commands without the following flags ( -type,

-lateral and -ten). Which diffusion will the above comands give? is it bulk
diffusion?

Gromacs manual:
-type:Compute diffusion coefficient in one direction:no, x, y or z
-lateral:Calculate the lateral diffusion in a plane perpendicular to: no,

x, y or z

-ten:Calculate the full tensor
2.) I plotted diffusions (10 values) as function of time. Diffusions dont

converge. Did I do any steps by mistake?

3.) From manual:
The diffusion constant is calculated by least squares fitting a straight

line (D*t + c)...

What is (D*t + c)? What are the meaning of D and c?
4.) What should be "Time between restarting points in trajectory"?

Thanks in advance
--
Ahmet Yıldırım





--
Ahmet Yıldırım




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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[gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

Dear users,

This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
-endfit -1 -b 10001 -e 2
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
-endfit -1 -b 20001 -e 3

g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
-endfit -1 -b 190001 -e 20

I have strange Diffusion results (especially 10,50,100,150,200 ns). How can
I fix this problem?
Results:
Time (ns) D(cm^2/s)
10 0.1616
20 0.0735
30 0.0775
40 0.1097
50 0.1471
60 0.0468
70 0.0667
80 0.0727
90 0.0664
100 0.1336
110 0.0899
120 0.0572
130 0.0506
140 0.0723
150 0.1466
160 0.0703
170 0.081
180 0.0278
190 0.1121
200 0.3136



2013/3/27 Ahmet yıldırım 
>
> Dear users,
>
> I used the following commands to get diffusion constants (every 10 ns) of
a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory
every 20 ps).  I looked at RMSD vs average structure, RMSD vs starting
structure, Radius of gyration, RMSD matrix. This simulation has reached to
converge at last 50 ns.
> g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1
> g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2
> g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3
> ...
> g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10
>
> 1.) I used the above commands without the following flags ( -type,
-lateral and -ten). Which diffusion will the above comands give? is it bulk
diffusion?
> Gromacs manual:
> -type:Compute diffusion coefficient in one direction:no, x, y or z
> -lateral:Calculate the lateral diffusion in a plane perpendicular to: no,
x, y or z
> -ten:Calculate the full tensor
> 2.) I plotted diffusions (10 values) as function of time. Diffusions dont
converge. Did I do any steps by mistake?
> 3.) From manual:
> The diffusion constant is calculated by least squares fitting a straight
line (D*t + c)...
> What is (D*t + c)? What are the meaning of D and c?
> 4.) What should be "Time between restarting points in trajectory"?
>
> Thanks in advance
> --
> Ahmet Yıldırım




--
Ahmet Yıldırım
--
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RE: [gmx-users] no CUDA-capable device is detected

[Berk Hess]

Hi,

I am not the expert on GPU detection, so we'll need to wait until an expert 
replies.
Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
mdrun -ntmpi 1 -gpu_id 0

Also your tpr file is from an older version. It will not run on a GPU.
You need to set the mdp option:
cutoff-scheme = Verlet
and run grompp to get a new tpr file.

Cheers,

Berk

> From: iitd...@gmail.com
> Date: Thu, 28 Mar 2013 14:57:16 +0530
> Subject: Re: [gmx-users] no CUDA-capable device is detected
> To: gmx-users@gromacs.org
> 
> On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess  wrote:
> 
> >
> > Hi,
> >
> > The code compiled, so the compiler is not the issue.
> >
> > I guess mdrun picked up GPU 0, which it should have ignored. You only want
> > to use GPU 1.
> >
> > Could you try running:
> > mdrun -ntmpi 1 -gpu_id 1
> >
> 
> $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr
> Note: file tpx version 73, software tpx version 83
> 
> NOTE: Error occurred during GPU detection:
>   no CUDA-capable device is detected
>   Can not use GPU acceleration, will fall back to CPU kernels.
> 
> 
> No GPUs detected
> 
> 
> ---
> Program mdrun_461, VERSION 4.6.1
> Source code file:
> /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580
> 
> Fatal error:
> Some of the requested GPUs do not exist, behave strangely, or are not
> compatible:
> GPU #1: inexistent
> 
> >
> > Cheers,
> >
> > berk
> >
> > > Date: Thu, 28 Mar 2013 10:51:58 +0200
> > > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > > From: g...@bioacademy.gr
> > > To: gmx-users@gromacs.org
> > >
> > > Hi Chandan
> > >
> > > Are you using the same version of GCC compiler that you used to compile
> > > CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think
> > there
> > > was some kind of incompatibility between the two).
> >
> 
> There is an work around with gcc 4.7.2. Please see
> http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html
> 
> >
> > > Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
> > > worked in my system (MacOS/Darwin).
> > >
> > > Just make sure to set the variables CC and CXX to point to the right
> > > compiler version when you run cmake.
> > >
> > > George
> > >
> > >
> > > > Dear GMX Users,
> > > >
> > > > I am trying to execute Gromacs 4.6.1 on one of the GPU server:
> > > > *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
> > > > *gcc*: 4.7.2
> > > >
> > > > CUDA Library paths
> > > > #CUDA-5.0
> > > > export CUDA_HOME=/usr/local/cuda-5.0
> > > > export PATH=$CUDA_HOME/bin:$PATH
> > > > export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH
> > > >
> > > > The gromacs has been compiled with
> > > >
> > > > CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0
> > cmake ..
> > > > -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single
> > > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461
> > -DGMX_LIBS_SUFFIX=_461
> > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> > > >
> > > > *Error on executing mdrun
> > > > *
> > > > *
> > > > *
> > > > *NOTE: Error occurred during GPU detection:
> > > > no CUDA-capable device is detected
> > > > Can not use GPU acceleration, will fall back to CPU kernels.
> > > >
> > > >
> > > > Will use 24 particle-particle and 8 PME only nodes
> > > > This is a guess, check the performance at the end of the log file
> > > > Using 32 MPI threads
> > > >
> > > > No GPUs detected
> > > >
> > > > *I checked my cuda installation. I am able to compile and execute the
> > > > sample programmes e.g., deviceQuery.
> > > >
> > > > Also executed *nvidia-smi *:
> > > > +--+
> > > > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 |
> > > >
> > |---+--+--+
> > > > | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
> > > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> > > >
> > |===+==+==|
> > > > | 0 NVS 300 | :03:00.0 N/A | N/A |
> > > > | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default |
> > > >
> > +---+--+--+
> > > > | 1 Tesla K20c | :04:00.0 Off | Off |
> > > > | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default |
> > > >
> > +---+--+--+
> > > >
> > > >
> > +-+
> > > > | Compute processes: GPU Memory |
> > > > | GPU PID Process name Usage |
> > > >
> > |=|
> > > > | 0 Not Supported |
> > > >
> > +-+
> > > >
> > > > What am I missing that Gromacs is not detecting the

Re: [gmx-users] no CUDA-capable device is detected

[Chandan Choudhury]

On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess  wrote:

>
> Hi,
>
> The code compiled, so the compiler is not the issue.
>
> I guess mdrun picked up GPU 0, which it should have ignored. You only want
> to use GPU 1.
>
> Could you try running:
> mdrun -ntmpi 1 -gpu_id 1
>

$mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr
Note: file tpx version 73, software tpx version 83

NOTE: Error occurred during GPU detection:
  no CUDA-capable device is detected
  Can not use GPU acceleration, will fall back to CPU kernels.


No GPUs detected


---
Program mdrun_461, VERSION 4.6.1
Source code file:
/home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580

Fatal error:
Some of the requested GPUs do not exist, behave strangely, or are not
compatible:
GPU #1: inexistent

>
> Cheers,
>
> berk
>
> > Date: Thu, 28 Mar 2013 10:51:58 +0200
> > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > From: g...@bioacademy.gr
> > To: gmx-users@gromacs.org
> >
> > Hi Chandan
> >
> > Are you using the same version of GCC compiler that you used to compile
> > CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think
> there
> > was some kind of incompatibility between the two).
>

There is an work around with gcc 4.7.2. Please see
http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html

>
> > Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
> > worked in my system (MacOS/Darwin).
> >
> > Just make sure to set the variables CC and CXX to point to the right
> > compiler version when you run cmake.
> >
> > George
> >
> >
> > > Dear GMX Users,
> > >
> > > I am trying to execute Gromacs 4.6.1 on one of the GPU server:
> > > *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
> > > *gcc*: 4.7.2
> > >
> > > CUDA Library paths
> > > #CUDA-5.0
> > > export CUDA_HOME=/usr/local/cuda-5.0
> > > export PATH=$CUDA_HOME/bin:$PATH
> > > export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH
> > >
> > > The gromacs has been compiled with
> > >
> > > CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0
> cmake ..
> > > -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single
> > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461
> -DGMX_LIBS_SUFFIX=_461
> > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> > >
> > > *Error on executing mdrun
> > > *
> > > *
> > > *
> > > *NOTE: Error occurred during GPU detection:
> > > no CUDA-capable device is detected
> > > Can not use GPU acceleration, will fall back to CPU kernels.
> > >
> > >
> > > Will use 24 particle-particle and 8 PME only nodes
> > > This is a guess, check the performance at the end of the log file
> > > Using 32 MPI threads
> > >
> > > No GPUs detected
> > >
> > > *I checked my cuda installation. I am able to compile and execute the
> > > sample programmes e.g., deviceQuery.
> > >
> > > Also executed *nvidia-smi *:
> > > +--+
> > > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 |
> > >
> |---+--+--+
> > > | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
> > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> > >
> |===+==+==|
> > > | 0 NVS 300 | :03:00.0 N/A | N/A |
> > > | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default |
> > >
> +---+--+--+
> > > | 1 Tesla K20c | :04:00.0 Off | Off |
> > > | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default |
> > >
> +---+--+--+
> > >
> > >
> +-+
> > > | Compute processes: GPU Memory |
> > > | GPU PID Process name Usage |
> > >
> |=|
> > > | 0 Not Supported |
> > >
> +-+
> > >
> > > What am I missing that Gromacs is not detecting the GPUs.
> > >
> > > Chandan
> > >
> > > --
> > > Chandan kumar Choudhury
> > > NCL, Pune
> > > INDIA
> > > --
> > > 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
> > >
> >
> >
> > Dr. George Patargias
> > Postdoctoral Researcher
> > Biomedical Research Foundation
> > Academy of Athens
> > 4, Soranou Ephessiou
> > 115 27
> > Athens
> > Greece
> >
> > Office: +302106597568
> >
> > --
> > gmx-users mailing listgm

[gmx-users] bond conversion between charmm and g96

[라지브간디]

p{margin:0;padding:0;}


Dear Justin,


Thank for your pointing out my issues. I just want to know how it can be 
converted.


I have referred the equation in chapter 4 and do not know exactly how I use 
them. 


For example, The C-O bond distance and force constant written as (0.112  and 
3.7000e+07 ) in gromos, whereas  in charmm27 written as ( 0.1128 and 933032.0). 


I found the equation for g96 type covalent potential Vb (rij) and force 
constant Fi(rij) and don't know how do i use this for above purpose? 


Could you elaborate an example how it can be done? Thanks a lot.







> Thanks for the mail justin. 
> 
> 
> In charmm27.ff, the value for bonded are in b0 and ko format, whereas the 
> gromos uses them in different way? If so, how do i convert between them? 
> 
> 
Please consult the manual, Chapters 4 and 5 for all the relevant equations 
and implementation. 


> 
> The value i incorporated for specific atoms are from published journals. 
> Thanks in advance. 
> 
> 
I think you're missing my point though. Just because something is 
published, doesn't mean you can use it for whatever purpose you like. 
People spend years working out properly balanced force fields, and if you 
try to put in some new atom type, it upsets the balance of every 
interaction. You may be OK within the context of CHARMM (depending on what 
the paper is, and what parameter set they modified), but I can guarantee 
you that if you're trying to incorporate CHARMM parameters into GROMOS, all 
you're doing is producing a pile of trash. You can probably "make it work" 
from a topology standpoint, but you shouldn't be doing it. I hope my 
perspective is clear; I'm trying to save you from wasted effort. 



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RE: [gmx-users] no CUDA-capable device is detected

[Berk Hess]

Hi,

The code compiled, so the compiler is not the issue.

I guess mdrun picked up GPU 0, which it should have ignored. You only want to 
use GPU 1.

Could you try running:
mdrun -ntmpi 1 -gpu_id 1

Cheers,

berk

> Date: Thu, 28 Mar 2013 10:51:58 +0200
> Subject: Re: [gmx-users] no CUDA-capable device is detected
> From: g...@bioacademy.gr
> To: gmx-users@gromacs.org
> 
> Hi Chandan
> 
> Are you using the same version of GCC compiler that you used to compile
> CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there
> was some kind of incompatibility between the two).
> 
> Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
> worked in my system (MacOS/Darwin).
> 
> Just make sure to set the variables CC and CXX to point to the right
> compiler version when you run cmake.
> 
> George
> 
> 
> > Dear GMX Users,
> >
> > I am trying to execute Gromacs 4.6.1 on one of the GPU server:
> > *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
> > *gcc*: 4.7.2
> >
> > CUDA Library paths
> > #CUDA-5.0
> > export CUDA_HOME=/usr/local/cuda-5.0
> > export PATH=$CUDA_HOME/bin:$PATH
> > export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH
> >
> > The gromacs has been compiled with
> >
> > CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake ..
> > -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single
> > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> >
> > *Error on executing mdrun
> > *
> > *
> > *
> > *NOTE: Error occurred during GPU detection:
> > no CUDA-capable device is detected
> > Can not use GPU acceleration, will fall back to CPU kernels.
> >
> >
> > Will use 24 particle-particle and 8 PME only nodes
> > This is a guess, check the performance at the end of the log file
> > Using 32 MPI threads
> >
> > No GPUs detected
> >
> > *I checked my cuda installation. I am able to compile and execute the
> > sample programmes e.g., deviceQuery.
> >
> > Also executed *nvidia-smi *:
> > +--+
> > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 |
> > |---+--+--+
> > | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
> > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> > |===+==+==|
> > | 0 NVS 300 | :03:00.0 N/A | N/A |
> > | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default |
> > +---+--+--+
> > | 1 Tesla K20c | :04:00.0 Off | Off |
> > | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default |
> > +---+--+--+
> >
> > +-+
> > | Compute processes: GPU Memory |
> > | GPU PID Process name Usage |
> > |=|
> > | 0 Not Supported |
> > +-+
> >
> > What am I missing that Gromacs is not detecting the GPUs.
> >
> > Chandan
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> > --
> > 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
> >
> 
> 
> Dr. George Patargias
> Postdoctoral Researcher
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
> 
> Office: +302106597568
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] no CUDA-capable device is detected

[George Patargias]

Hi Chandan

Are you using the same version of GCC compiler that you used to compile
CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there
was some kind of incompatibility between the two).

Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
worked in my system (MacOS/Darwin).

Just make sure to set the variables CC and CXX to point to the right
compiler version when you run cmake.

George


> Dear GMX Users,
>
> I am trying to execute Gromacs 4.6.1 on one of the GPU server:
> *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
> *gcc*: 4.7.2
>
> CUDA Library paths
> #CUDA-5.0
> export CUDA_HOME=/usr/local/cuda-5.0
> export PATH=$CUDA_HOME/bin:$PATH
> export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH
>
> The gromacs has been compiled with
>
> CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake ..
> -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single
> -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>
> *Error on executing mdrun
> *
> *
> *
> *NOTE: Error occurred during GPU detection:
> no CUDA-capable device is detected
> Can not use GPU acceleration, will fall back to CPU kernels.
>
>
> Will use 24 particle-particle and 8 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 32 MPI threads
>
> No GPUs detected
>
> *I checked my cuda installation. I am able to compile and execute the
> sample programmes e.g., deviceQuery.
>
> Also executed *nvidia-smi *:
> +--+
> | NVIDIA-SMI 4.310.40 Driver Version: 310.40 |
> |---+--+--+
> | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> |===+==+==|
> | 0 NVS 300 | :03:00.0 N/A | N/A |
> | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default |
> +---+--+--+
> | 1 Tesla K20c | :04:00.0 Off | Off |
> | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default |
> +---+--+--+
>
> +-+
> | Compute processes: GPU Memory |
> | GPU PID Process name Usage |
> |=|
> | 0 Not Supported |
> +-+
>
> What am I missing that Gromacs is not detecting the GPUs.
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> --
> 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
>


Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568

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[gmx-users] retraining multiple protein ligand interactions using pull-code

[Saravanan]

Hello everyone,

I am new to using gromacs. I am currently studying an enzyme catalysing a
transfer reaction. there are two substrates and I want to restraint
specific interactions between different parts of the ligands and the
protein. As I understand so far from reading various discussions in the
group, restraining such interactions is possible through pull code, But we
can assign only one pull group0, I am wondering if there is better way to
restraint multiple interactions between multiple molecules in a single
simulation. If not through pull-code, what will be the best way to ensure
many specific intermolecular restraints?

thank you very much in advance.

regards,
Saravanan
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