date:20130501

Re: [gmx-users] local pressure

2013-05-01 Thread XAvier Periole


What are you looking for? Have a look at the papers they might be inspiring :))

On May 1, 2013, at 10:33 PM, Sikandar Mashayak  wrote:

> Ok, I did rerun with local pressure mdrun, and got pressure.dat* files in
> binary format. how do I proceed from here? Any utility to analyze or
> post-process this?
> 
> 
> On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak 
> wrote:
> 
>> Thanks Xavier,
>> 
>> I will give it a try.
>> 
>> 
>> On Wed, May 1, 2013 at 10:56 AM, XAvier Periole  wrote:
>> 
>>> 
>>> 
>>> Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are
>>> :)).
>>> 
>>> The paper related to the use would be:
>>> Ollila et al, PRL 102, 078101 (2009)
>>> Ollila et al, Biophysical Journal (100)1651–59
>>> 
>>> On May 1, 2013, at 5:48 PM, Sikandar Mashayak 
>>> wrote:
>>> 
 Thanks Xavier
 
 
 Can you please elaborate on how to use and post-process the local
>>> pressure
 version of gromacs? Do you have any examples or reference article?
 
 May be you can create a HowTo wiki as Justin suggested, it would be of
 great help.
 
 Thanks
 Sikandar
 
 
 On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul  wrote:
 
> 
> 
> On 5/1/13 5:12 AM, XAvier Periole wrote:
> 
>> 
>> The use of the original code is quite straightforward, the post
>> processing is a bit more confusing but quite accessible.
>> 
>> 
> That would be a great topic for a wiki How-To.
> 
> 
> We have been using this code (the one available on the site) and
>>> related
>> version in the lab and we definitely would find it very sad to not
>>> keep
>> this feature available in GROMACS.
>> 
>> 
> I never said it would go away, but given the fact that there have been
>>> no
> updates to the git branch in over 3 years, it's simply unlikely that
>>> anyone
> has cared to move it forward.  If someone wants to update the code to
>>> be
> compatible with 4.6, that would be a welcome contribution.  Lack of any
> request for improvements and inclusion in an official release has
>>> likely
> led to the decline in interest from the development team.  If you want
> something included, you should file a feature request on
> redmine.gromacs.org - it's the only official way we keep track of
>>> fixes
> and features.  If it's not there, it likely won't get addressed until
>>> one
> of the developers has a compelling need to work on it.
> 
> -Justin
> 
> 
> On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:
>> 
>> 
>>> 
>>> On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
>>> 
 Hi
 
 I found the branch of gromacs code called localpressure-4.0 at
 http://redmine.gromacs.org/**projects/gromacs/repository/**
 show?rev=localpressure-4-0<
>>> http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0
 
 .
 I am wondering whether this code can compute the spatial variation
>>> of
 pressure in given system. And if it does, how stable is this
>>> branch? Are
 there any known issues with it? And any particular reason this is
>>> not
 included in main gromacs releases?
 
 
>>> Lack of documentation has made it very difficult to use, it is
>>> extremely
>>> slow, and no one ever asks about it except once every few years.
>>> All of
>>> those factors make it unlikely to ever incorporate into an actual
>>> release.
>>> Given that the development process has gone on for years in the
>>> absence of
>>> any real interest in the localpressure branch, it's probably more
>>> trouble
>>> than it's worth to get it up and running effectively.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==**==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> 
>>> ==**==
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<
>>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>>> http://www.gromacs.org/Support/Mailing_Lists>
>>> 
>> 
>> 
> --
> ==**==
> 
> Justin A. Le

[gmx-users] Temperature for individual amino acid residues

2013-05-01 Thread bipin singh

Hi All,

I want to calculate temperature for each individual amino acids residues
present in a protein after the simulation. I know that this can be done
with help of g_traj, but my concern is whether this will give me correct
temperature or not because it was mentioned that g_traj
does not mind the constraints. Please let me know what type of correction
need to done on the output from g_traj if we need correct temperature
values.
OR
Is there any way to get it from .edr file...

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

[gmx-users] PMF calculation between protein and ligand

2013-05-01 Thread Arunima Shilpi

Sir

I have query as to how to go ahead for potential mean force (PMF)
calculation between protein and ligand. As per the umbrella sampling
protocol you have provided us in gromacs tutotrial it says it is for
protein molecules...

-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] surrounding a peptide by ions of magnesium

2013-05-01 Thread Mohan maruthi sena

Hi all,
   I have system consisting of a peptide(alpha-helix), I want the
peptide to be surrounded by magnesium ions(instead of water). How can i do
this gromacs? How can I find the concentration of magnesium ions. just like
in solution we have 0.5 Molar  Mg+2  solution, My question how can  find
concentration by increasing number of ions.

Thanks for a reply in advance,

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

Re: [gmx-users] Gromacs mpi error while running REMD

2013-05-01 Thread Justin Lemkul




On 5/1/13 7:50 PM, bharat gupta wrote:

Dear gmx-users,

I got the following error after issuing the final command for running 12
replicas :-

[bme:42039] *** Process received signal ***
[bme:42039] Signal: Segmentation fault (11)
[bme:42039] Signal code: Invalid permissions (2)
[bme:42039] Failing at address: 0x7f093b655340
[bme:42039] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42039] [ 1]
/opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x2337)
[0x7f093c281fa7]
[bme:42039] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
[0x7f093c2175d6]
[bme:42039] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
[0x7f093ca47b3a]
[bme:42039] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
[0x7f093cadc6f7]
[bme:42039] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42039] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42039] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42039] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42039] [ 9] mdrun() [0x405a29]
[bme:42039] *** End of error message ***
Wrote pdb files with previous and current coordinates
[bme:42036] *** Process received signal ***
[bme:42036] Signal: Segmentation fault (11)
[bme:42036] Signal code: Invalid permissions (2)
[bme:42036] Failing at address: 0x7f794bbe3800
[bme:42036] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42036] [ 1]
/opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x13e2)
[0x7f794c4b8052]
[bme:42036] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
[0x7f794c44e5d6]
[bme:42036] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
[0x7f794cc7eb3a]
[bme:42036] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
[0x7f794cd136f7]
[bme:42036] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42036] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42036] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42036] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42036] [ 9] mdrun() [0x405a29]
[bme:42036] *** End of error message ***
[bme:42042] *** Process received signal ***
[bme:42042] Signal: Segmentation fault (11)
[bme:42042] Signal code: Address not mapped (1)
[bme:42042] Failing at address: 0x7f119c3b96b0
[bme:42042] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42042] [ 1]
/opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1345)
[0x7f11972e2fb5]
[bme:42042] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
[0x7f11972795d6]
[bme:42042] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
[0x7f1197aa9b3a]
[bme:42042] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
[0x7f1197b3e6f7]
[bme:42042] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42042] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42042] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42042] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42042] [ 9] mdrun() [0x405a29]
[bme:42042] *** End of error message ***




Check your .log file and/or stderr for more informative, Gromacs-specific error 
messages.  The backtrace suggests your system is probably blowing up.


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--


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


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

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

[gmx-users] Gromacs mpi error while running REMD

2013-05-01 Thread bharat gupta

Dear gmx-users,

I got the following error after issuing the final command for running 12
replicas :-

[bme:42039] *** Process received signal ***
[bme:42039] Signal: Segmentation fault (11)
[bme:42039] Signal code: Invalid permissions (2)
[bme:42039] Failing at address: 0x7f093b655340
[bme:42039] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42039] [ 1]
/opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x2337)
[0x7f093c281fa7]
[bme:42039] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
[0x7f093c2175d6]
[bme:42039] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
[0x7f093ca47b3a]
[bme:42039] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
[0x7f093cadc6f7]
[bme:42039] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42039] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42039] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42039] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42039] [ 9] mdrun() [0x405a29]
[bme:42039] *** End of error message ***
Wrote pdb files with previous and current coordinates
[bme:42036] *** Process received signal ***
[bme:42036] Signal: Segmentation fault (11)
[bme:42036] Signal code: Invalid permissions (2)
[bme:42036] Failing at address: 0x7f794bbe3800
[bme:42036] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42036] [ 1]
/opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x13e2)
[0x7f794c4b8052]
[bme:42036] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
[0x7f794c44e5d6]
[bme:42036] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
[0x7f794cc7eb3a]
[bme:42036] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
[0x7f794cd136f7]
[bme:42036] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42036] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42036] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42036] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42036] [ 9] mdrun() [0x405a29]
[bme:42036] *** End of error message ***
[bme:42042] *** Process received signal ***
[bme:42042] Signal: Segmentation fault (11)
[bme:42042] Signal code: Address not mapped (1)
[bme:42042] Failing at address: 0x7f119c3b96b0
[bme:42042] [ 0] /lib64/libpthread.so.0() [0x329220f500]
[bme:42042] [ 1]
/opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1345)
[0x7f11972e2fb5]
[bme:42042] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
[0x7f11972795d6]
[bme:42042] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
[0x7f1197aa9b3a]
[bme:42042] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
[0x7f1197b3e6f7]
[bme:42042] [ 5] mdrun(do_md+0x6a45) [0x42c245]
[bme:42042] [ 6] mdrun(mdrunner+0xa59) [0x421309]
[bme:42042] [ 7] mdrun(main+0x12fd) [0x4317dd]
[bme:42042] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
[bme:42042] [ 9] mdrun() [0x405a29]
[bme:42042] *** End of error message ***



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

Re: [gmx-users] g_msd for many molecules

2013-05-01 Thread Dr. Vitaly Chaban

The resulting MSD will correspond to the average from individual atoms.

Calculating MSD of an individual atom and ascribing it to a [small]
molecule, which this atom belongs to, is reasonable. Assuming that averaged
MSD from atoms correspond to the cluster they form is not.


Dr. Vitaly Chaban




On Wed, May 1, 2013 at 2:40 PM, George Patargias  wrote:

> Hello
>
> I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
> g_msd. If I include the atoms of all these 8 molecules as a single group
> in the index file, will g_msd calculate the MSD of the center of mass of
> them or it will average over all atoms?
>
>
> Thanks
> George
>
>
> 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
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_msd for many molecules

2013-05-01 Thread Justin Lemkul




On 5/1/13 8:40 AM, George Patargias wrote:

Hello

I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
g_msd. If I include the atoms of all these 8 molecules as a single group
in the index file, will g_msd calculate the MSD of the center of mass of
them or it will average over all atoms?



The calculation considers all the atoms, not just their COM.

-Justin

--


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


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

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

Re: [gmx-users] help with g_hydorder and g_polystat

2013-05-01 Thread Justin Lemkul




On 5/1/13 8:44 AM, Emmanuel, Alaina wrote:


No, using a trajectory file with g_hydorder hasn't made any difference. The 
error is still the same.

When I use g_polystat, I use the following command:

g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg 
-o polystat.xvg

Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than 
using the whole polymer structure in an index file.



The g_hydorder problem is a bug in the code and I have filed a bug report on 
Redmine.  I have no insight into what's going on with g_polystat, sorry.


-Justin

--


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


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

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

Re: [gmx-users] minimization of particular residue/atom

2013-05-01 Thread Mark Abraham

On Wed, May 1, 2013 at 4:20 PM, gromacs query wrote:

> Dear All,
>
> I am using Charmm gui built membrane (120 x 2). But during minimization I
> was getting error.
>
> Potential Energy  =  4.6809051e+19
> Maximum force =inf on atom 4281
> Norm of force =inf
>
>
> (inf means? means infinite/NAN)
>

All the above means your system is
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

I removed the  full lipid residue having atom number 4281. I was again
> getting error representing some other atoms so finally I removed three
> lipid residues. Doing this I was able to complete convergence.
>
> I have two queries:
>
> 1) As I have removed three residues from Charmm gui membrane, does this
> affect final results? Although I will be doing MD for membrane first.
>

Maybe. We don't know whether the membrane was built wrongly, or you
post-processed the coordinate file wrongly, or whether you need all the
lipid molecules to achieve the right density, or...


> 2) Also is there any way so that particular atoms can be minimized or
> ''touched'' ? Here in this case I removed three lipid residues but this
> will not be good say in case of proteins. Just as a analogy if this problem
> arises  in AMBER (rather I faced such problem many times) I can use xleap
> and can move atom a little and relax it particularly by selecting it , so
> that later if use the edited structure I get convergence properly without
> error.
>

You can only do that by moving the coordinates by hand in the coordinate
file before you give it to grompp. Your PE above is so large that this is
not the right approach to fix the problem. I would guess your periodic box
is not the one you were intended to use.

Mark


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

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

2013-05-01 Thread Mark Abraham

On Wed, May 1, 2013 at 2:32 PM, Reza Salari  wrote:

> Hi Justin,
>
> I actually did :) but it ended up being bigger than 50 kb so it needed
> moderator approval to show up. I was hoping it would've been released by
> now. I'll attach a the details below.
>
> Any help/hint is highly appreciated.
>
> Reza
>
> Details:
>
> *1)* Both systems were prepared using VMD "membrane" package and then
> waters were removed. I used Gromacs 4.6.1 and NAMD 2.9.
>
> *2)* Simulations were run in vacuum as a single-point energy calculations
> (0 step).


No, they weren't. See
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
You cannot hope to reproduce accurately the energy of a configuration if
you let the coordinates be manipulated.

PME was not used.
>
> *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the
> output was saved as the pdb format. The mdp file:
>
> integrator= md
> nsteps= 0
> nstlog  = 1
> nstlist= 1
> ns_type= grid
> rlist= 100.0
> coulombtype= cut-off
> rcoulomb= 100.0
> rvdw= 100.0
> pbc = no
>
> *4) *NAMD input file:
>
> structure  ../0_prep/memb_nowat.psf
> paratypecharmm  on
> parameterspar_all27_prot_lipid.prm
> exclude scaled1-4
> 1-4scaling 1.0
> switching off
> switchdist 8
> cutoff 1000
> pairlistdist 1000
> margin 0
> timestep 1.0
> outputenergies 1
> outputtiming 1
> binaryoutput no
> coordinates ../0_prep/memb_nowat.pdb
> outputname out
> dcdfreq 10
> temperature 300
> run 0
>
> *5)* Energies:
>
> For Single POPC  (kcal/mol)
>
>
> Gromacs NAMD Diff
>
> Bond 43.0022 43.0015 -0.0007
> Angle 80.6568 80.6571 0.0003
> Dih 29.8083 29.8083 0.
> Imp 0.8452 0.8452 0.
>
> Coul -17.2983 -17.2983 0.
> LJ -7.0798 -7.0798 0.
>
> Pot 129.9343 129.9340 -0.0003
>
>
The intra-molecule terms look fine. Since this is a lipid, there are
non-bonded interactions that are intra-molecule, so the non-bondeds also
seem fine.

For POPC Memb (kcal/mol)
>
> Gromacs NAMD Diff
>
> Bond 1539.1181 1539.1162 -0.0019
> Angle 3111.9264 3111.9197 -0.0067
> Dih 1250.5425 1250.5421 -0.0004
> Imp 16.2837 16.2837 0.
>
> Coul -1837.8585 -1705.3075 132.5510
> LJ -995.0311   -1219.3432 -224.3121
>
> Pot 3084.9904 2993.2110 -91.7794
>

Something you think is equivalent is not :-) Move to testing a system with
two lipids. Inspect all the logfile outputs very carefully for clues.

Mark


>
>
>
>
>
> On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/30/13 4:19 PM, Reza Salari wrote:
> >
> >> Hi
> >>
> >> I have set up two small systems, one with a single POPC lipid, and
> another
> >> system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
> >> similar comparison as in Table 1 in the Par Bjelkmar et al paper
> (porting
> >> charmm ff to gromacs) for my systems. My main question is that for the
> >> single POPC, all the potential energy terms match very well, but for the
> >> membrane system the non-bonding terms differ significantly.
> >>
> >> I am providing the full details below and greatly appreciate any hint
> for
> >> better comparison of the energies.
> >>
> >>
> >> Thanks,
> >> Reza Salari
> >>
> >> Details:
> >>
> >> 1) Both systems were prepared using VMD "membrane" package:
> >>
> >> 2)
> >>
> >>
> > It appears you hit "send" too early.  Please provide the entirety of the
> > details you intended.  Complete .mdp files and actual quantification of
> the
> > differences you are observing are also very important.
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> 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/Su

Re: [gmx-users] Re: Using virtual site

2013-05-01 Thread Mark Abraham

On Wed, May 1, 2013 at 3:16 PM, 라지브간디  wrote:

> Dear
> Mark,
>
>
>
>
> As per you suggestion, I have simulated a single CO as well as
> CO-with-vsite in a box.
>
>
>
>
> A single CO runs without any problem, BUT the CO-with-vsite
> gives an same error as before:
>
>
>
>
> Steepest
> Descents:
>
>Tolerance (Fmax)   =
>  1.0e+03
>
>Number of steps=
>  5
>
> Step=0, Dmax= 1.0e-02 nm, Epot=
> -3.73341e+04 Fmax= 3.38911e+05, atom= 2
>
> Step=1, Dmax= 1.0e-02 nm, Epot=
> -4.54970e+04 Fmax= 4.95889e+05, atom= 2
>
> Step=2, Dmax= 1.2e-02 nm, Epot=
> -6.18180e+04 Fmax= 9.34585e+05, atom= 2
>
> Step=3, Dmax= 1.4e-02 nm, Epot=
> -1.10395e+05 Fmax= 3.03088e+06, atom= 1
>
> Step=5, Dmax= 8.6e-03 nm, Epot=
> -2.09874e+05 Fmax= 1.09138e+07, atom= 2
>
> Step=9, Dmax= 1.3e-03 nm, Epot=
> -2.42526e+05 Fmax= 1.45550e+07, atom= 1
>
> Step=   11, Dmax= 7.8e-04 nm, Epot=
> -2.67493e+05 Fmax= 1.76910e+07, atom= 2
>
> Step=   14, Dmax= 2.3e-04 nm, Epot=
> -2.76005e+05 Fmax= 1.88299e+07, atom= 2
>
> Step=   16, Dmax= 1.4e-04 nm, Epot=
> -2.81365e+05 Fmax= 1.95651e+07, atom= 2
>
> Step=   19, Dmax= 4.2e-05 nm, Epot=
> -2.83032e+05 Fmax= 1.97967e+07, atom= 1
>
> Step=   23, Dmax= 6.3e-06 nm, Epot=
> -2.83281e+05 Fmax= 1.98315e+07, atom= 1
>
> Step=   26, Dmax= 1.9e-06 nm, Epot=
> -2.83355e+05 Fmax= 1.98418e+07, atom= 2
>
> Step=   28, Dmax= 1.1e-06 nm, Epot=
>nan Fmax= 0.0e+00, atom= 0
>
> Stepsize too small, or no change in energy.
>
> Converged to machine precision,
>
> but not to the requested precision Fmax < 1000
>
>
>
>
> Double precision normally gives you higher
> accuracy.
>
>
>
>
> writing lowest energy coordinates.
>
>
>
>
> Back Off! I just backed up min.gro to ./#min.gro.1#
>
>
>
>
> Steepest Descents converged to machine precision in
> 29 steps,
>
> but did not reach the requested Fmax < 1000.
>
> Potential Energy  = -2.8335531e+05
>
> Maximum force =  1.9841798e+07
> on atom 2
>
> Norm of force =  1.6200760e+07
>
>
>
>
>
>
>
> I am afraid that I am a making any mistakes of setting the
> vsite?
>
>
>
>
>
> My
> topology file vsite setting :
>
>
>
>
> [ moleculetype ]
>
>
> ;
> Namenrexcl
>
> Other_chain_A   3
>
>
>
> [ atoms ]
>
> ;   nr   type  resnr
> residue  atom   cgnr charge   mass
>  typeBchargeB  massB
>
> ; residue 157 CMO rtp CMO  q -1.6
>
>  1
>  C157CMO  C
>  1  -0.75 12.011   ; qtot -0.75
>
>  2
>  O157CMO  O
>  2  -0.8515.9994   ; qtot -1.6
>
>  3
>  I 157 CMO  I
>   3   1.6  0.
>
> [ bonds ]
>
> ;  aiaj funct
>c0c1
>c2
>  c3
>
> 1 2 2
>gb_4
>
> [ virtual_sites2 ]
>
> ; Vsite fromfunct
>   a
>
>
>
>
> 3   1 2
> 1   0.4376625
>
>
>
>
>
>
>
> My coordiante (.gro) file where i added the vsite xyz: Also included
> the vsite atom info in atomypes as well as ffnonbonded.itp.
>
>
>
>
> Gravel
> Rubs Often Many Awfully Cauterized Sores
>
>
>   3
>
>
> 157CMO  C1   1.625   2.697
> 0.490
>
>
> 157CMO  O2   1.722   2.647
> 0.482
>
>
> 157CMO   I 3   1.673   2.672
>   0.486
>
>  0.09660
>   0.05040   0.00760
>
>
This box is far too small.

Mark


> ~
>
>
>
>
>
>
> Could you tell what mistakes I am making here ?
>
>
>
>
>
> Thanks in advance.
>
>
>
>
>
> Raju
>
>
>
>
>
> On Wed, May 1, 2013 at ��� :
>
>
>
> I mean simulate a single CO in a box. Then CO-with-vsite in a box.
> If you
> can do that, then a bunch of problems are known to be solved. Leaping in
> the deep end with a complex system means you don't know where the trouble
> comes from when you have it.
>
> Mark
>
> On Wed, May 1, 2013 at 8:45 AM, ���
>  wrote:
>
> > Dear Mark,
> >
> > > You mean do the CO simulation and then add V-site upon
> production run?
> >
> > Could you please more specific, what has to be done to avoid this
> error?
> >
> >  >
> > On Fri, Apr 26, 2013 at 6:16 PM, ��
>  wrote:
> >
> > Maybe your starting configuration of atoms is too broken to be
> useful.
> > Maybe you have some interaction on atom 2513 that doesn't work.
> >
> > Make a simple system of CO work, then do CO+vsite. Then apply those
> lessons
> > to your complex system.
> >
> > Mark
> >
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users 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.

Re: [gmx-users] stable branch using git

2013-05-01 Thread Mark Abraham

On Wed, May 1, 2013 at 5:40 PM, Sikandar Mashayak wrote:

> Thanks Justin and Mark
>
> I think I would checkout and create a branch from v4.6 tag.
>

You don't need a branch until you are going to develop something. And there
is no reason to make an install of an old point release for new work when
bugs are fixed and available in 4.6.1.

One more thing, would it be an issue if I install mulitple
> version's/branche's binaries and libraries in the same folder with branch
> specific suffixes to distinguish between them?
>

You can do that. Or install into different directories and source the GMXRC
from the version you wish to use. Since you'll have to source a GMXRC
anyway, you may as well do the latter and not have to write scripts/command
lines that specify the version on every command.

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

Re: [gmx-users] local pressure

2013-05-01 Thread Sikandar Mashayak

Ok, I did rerun with local pressure mdrun, and got pressure.dat* files in
binary format. how do I proceed from here? Any utility to analyze or
post-process this?


On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak wrote:

> Thanks Xavier,
>
> I will give it a try.
>
>
> On Wed, May 1, 2013 at 10:56 AM, XAvier Periole  wrote:
>
>>
>>
>> Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are
>> :)).
>>
>> The paper related to the use would be:
>> Ollila et al, PRL 102, 078101 (2009)
>> Ollila et al, Biophysical Journal (100)1651–59
>>
>> On May 1, 2013, at 5:48 PM, Sikandar Mashayak 
>> wrote:
>>
>> > Thanks Xavier
>> >
>> >
>> > Can you please elaborate on how to use and post-process the local
>> pressure
>> > version of gromacs? Do you have any examples or reference article?
>> >
>> > May be you can create a HowTo wiki as Justin suggested, it would be of
>> > great help.
>> >
>> > Thanks
>> > Sikandar
>> >
>> >
>> > On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul  wrote:
>> >
>> >>
>> >>
>> >> On 5/1/13 5:12 AM, XAvier Periole wrote:
>> >>
>> >>>
>> >>> The use of the original code is quite straightforward, the post
>> >>> processing is a bit more confusing but quite accessible.
>> >>>
>> >>>
>> >> That would be a great topic for a wiki How-To.
>> >>
>> >>
>> >> We have been using this code (the one available on the site) and
>> related
>> >>> version in the lab and we definitely would find it very sad to not
>> keep
>> >>> this feature available in GROMACS.
>> >>>
>> >>>
>> >> I never said it would go away, but given the fact that there have been
>> no
>> >> updates to the git branch in over 3 years, it's simply unlikely that
>> anyone
>> >> has cared to move it forward.  If someone wants to update the code to
>> be
>> >> compatible with 4.6, that would be a welcome contribution.  Lack of any
>> >> request for improvements and inclusion in an official release has
>> likely
>> >> led to the decline in interest from the development team.  If you want
>> >> something included, you should file a feature request on
>> >> redmine.gromacs.org - it's the only official way we keep track of
>> fixes
>> >> and features.  If it's not there, it likely won't get addressed until
>> one
>> >> of the developers has a compelling need to work on it.
>> >>
>> >> -Justin
>> >>
>> >>
>> >> On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:
>> >>>
>> >>>
>> 
>>  On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
>> 
>> > Hi
>> >
>> > I found the branch of gromacs code called localpressure-4.0 at
>> > http://redmine.gromacs.org/**projects/gromacs/repository/**
>> > show?rev=localpressure-4-0<
>> http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0
>> >
>> > .
>> > I am wondering whether this code can compute the spatial variation
>> of
>> > pressure in given system. And if it does, how stable is this
>> branch? Are
>> > there any known issues with it? And any particular reason this is
>> not
>> > included in main gromacs releases?
>> >
>> >
>>  Lack of documentation has made it very difficult to use, it is
>> extremely
>>  slow, and no one ever asks about it except once every few years.
>>  All of
>>  those factors make it unlikely to ever incorporate into an actual
>> release.
>>  Given that the development process has gone on for years in the
>> absence of
>>  any real interest in the localpressure branch, it's probably more
>> trouble
>>  than it's worth to get it up and running effectively.
>> 
>>  -Justin
>> 
>>  --
>>  ==**==
>> 
>>  Justin A. Lemkul, Ph.D.
>>  Research Scientist
>>  Department of Biochemistry
>>  Virginia Tech
>>  Blacksburg, VA
>>  jalemkul[at]vt.edu | (540) 231-9080
>>  http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> 
>>  ==**==
>>  --
>>  gmx-users mailing listgmx-users@gromacs.org
>>  http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>  * Please search the archive at http://www.gromacs.org/**
>>  Support/Mailing_Lists/Search<
>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>  * Please don't post (un)subscribe requests to the list. Use the www
>>  interface or send it to gmx-users-requ...@gromacs.org.
>>  * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> http://www.gromacs.org/Support/Mailing_Lists>
>> 
>> >>>
>> >>>
>> >> --
>> >> ==**==
>> >>
>> >> Justin A. Lemkul, Ph.D.
>> >> Research Scientist
>> >> Department of Biochemistry
>> >> Virginia Tech
>> >> Blacksburg, VA
>> >> jalemkul[at]vt.edu | (540) 231-9080
>> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanla

Re: [gmx-users] issue in replica exchange

2013-05-01 Thread XAvier Periole

Ok here is my current status on that REMD issue. 

For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps, 
time step: dt=0.002 - 0.020 fs, 
COM removal on for bilayer/water separately

The symptoms: explosion of the system after 2-5 steps following the swap, first 
sign is a huge jump in LJ interactions and pressure. This jump seems to be 
absorbed by the box size and temperature when possible … see example I provided 
earlier. A large VCM (velocity centre of mass?) is often associated with the 
crash. But also pressure scaling more than 1% ...

1- the problem mentioned above remains in gmx-4.5.7 and it might actually got 
worse. I was able to run a 500 ns simulation with gmx405 using similar setup as 
for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in the 
following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally to 
the remd gromacs by getting the gro file with the mdp adjusting the 
temperature) it goes all fine. 
4- the issue gets much worst when the consecutive replicas differ (different 
protein conformations and the box size etc) … explosion at first exchange. 
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2 
steps). All exchanges accepted at first attempt crash with the message "Large 
VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD 
simulation after equilibration in the same NVT ensemble (for 1 ns) removes the 
problem. 
9- taking the equilibrated NVT conformations, equilibrate them in an NPT 
ensemble (1 ns) and let go the exchanges afterwards restores the problem … one 
exchange is not properly done at the second trial, while the first ones were 
fine. Well if errors were made that was with reasonable 
10- note also that the coarse grain I use is extremely forgiving, meaning you 
can perform really nasty transformations and run it further after simple 
minimisation … so even abrupt changes in temperatures should be fine and relax 
quickly. 
11- when looking at the conformations themselves nothing appears to have jumped 
over or nothing funky. 

At this point I am not sure what to think and what to do next. There is 
definitely something not going right during the exchanges. 

Anyone has been able to run a REMD simulation in an NPT ensemble without 
crashes? I would imagine someone has and something particular to my system is 
making it going wrong but I am really wondering what it could be. My feeling is 
that something relative to the box size or pressure is not going across but it 
might be something completely different, when the consecutive systems differ 
reasonably. 

However that would suggest that the manner the exchanges are made is severely 
wrong in some cases. 

Any help to resolve the problem would be greatly appreciated.

XAvier.

On Apr 26, 2013, at 9:21 AM, Mark Abraham  wrote:

> On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole  wrote:
> 
>> 
>> Thanks for the answer. I'll check gmx4.5.7 and report back.
>> 
>> I am not sure what you mean by GROMACS swaps the coordinates not the
>> ensemble data. The coupling to P and T and not exchanged with it?
> 
> 
> The code in src/kernel/repl_ex.c:
> 
> static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
> {
>/* When t_state changes, this code should be updated. */
>int ngtc, nnhpres;
>ngtc= state->ngtc * state->nhchainlength;
>nnhpres = state->nnhpres* state->nhchainlength;
>exchange_rvecs(ms, b, state->box, DIM);
>exchange_rvecs(ms, b, state->box_rel, DIM);
>exchange_rvecs(ms, b, state->boxv, DIM);
>exchange_reals(ms, b, &(state->veta), 1);
>exchange_reals(ms, b, &(state->vol0), 1);
>exchange_rvecs(ms, b, state->svir_prev, DIM);
>exchange_rvecs(ms, b, state->fvir_prev, DIM);
>exchange_rvecs(ms, b, state->pres_prev, DIM);
>exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
>exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
>exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
>exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
>exchange_doubles(ms, b, state->therm_integral, state->ngtc);
>exchange_rvecs(ms, b, state->x, state->natoms);
>exchange_rvecs(ms, b, state->v, state->natoms);
>exchange_rvecs(ms, b, state->sd_X, state->natoms);
> }
> 
> I mis-stated last night - there *is* exchange of ensemble data, but it is
> incomplete. In particular, state->ekinstate is not exchanged. Probably it
> is incomplete because the 9-year-old comment about t_state changing is in a
> location that nobody changing t_state will see. And serializing a complex C
> data structure over MPI is tedious at best. But that is not really an
> excuse for the non-modularity GROMACS h

Re: [gmx-users] local pressure

2013-05-01 Thread Sikandar Mashayak

Thanks Xavier,

I will give it a try.


On Wed, May 1, 2013 at 10:56 AM, XAvier Periole  wrote:

>
>
> Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are
> :)).
>
> The paper related to the use would be:
> Ollila et al, PRL 102, 078101 (2009)
> Ollila et al, Biophysical Journal (100)1651–59
>
> On May 1, 2013, at 5:48 PM, Sikandar Mashayak 
> wrote:
>
> > Thanks Xavier
> >
> >
> > Can you please elaborate on how to use and post-process the local
> pressure
> > version of gromacs? Do you have any examples or reference article?
> >
> > May be you can create a HowTo wiki as Justin suggested, it would be of
> > great help.
> >
> > Thanks
> > Sikandar
> >
> >
> > On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 5/1/13 5:12 AM, XAvier Periole wrote:
> >>
> >>>
> >>> The use of the original code is quite straightforward, the post
> >>> processing is a bit more confusing but quite accessible.
> >>>
> >>>
> >> That would be a great topic for a wiki How-To.
> >>
> >>
> >> We have been using this code (the one available on the site) and related
> >>> version in the lab and we definitely would find it very sad to not keep
> >>> this feature available in GROMACS.
> >>>
> >>>
> >> I never said it would go away, but given the fact that there have been
> no
> >> updates to the git branch in over 3 years, it's simply unlikely that
> anyone
> >> has cared to move it forward.  If someone wants to update the code to be
> >> compatible with 4.6, that would be a welcome contribution.  Lack of any
> >> request for improvements and inclusion in an official release has likely
> >> led to the decline in interest from the development team.  If you want
> >> something included, you should file a feature request on
> >> redmine.gromacs.org - it's the only official way we keep track of fixes
> >> and features.  If it's not there, it likely won't get addressed until
> one
> >> of the developers has a compelling need to work on it.
> >>
> >> -Justin
> >>
> >>
> >> On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:
> >>>
> >>>
> 
>  On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
> 
> > Hi
> >
> > I found the branch of gromacs code called localpressure-4.0 at
> > http://redmine.gromacs.org/**projects/gromacs/repository/**
> > show?rev=localpressure-4-0<
> http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0
> >
> > .
> > I am wondering whether this code can compute the spatial variation of
> > pressure in given system. And if it does, how stable is this branch?
> Are
> > there any known issues with it? And any particular reason this is not
> > included in main gromacs releases?
> >
> >
>  Lack of documentation has made it very difficult to use, it is
> extremely
>  slow, and no one ever asks about it except once every few years.  All
> of
>  those factors make it unlikely to ever incorporate into an actual
> release.
>  Given that the development process has gone on for years in the
> absence of
>  any real interest in the localpressure branch, it's probably more
> trouble
>  than it's worth to get it up and running effectively.
> 
>  -Justin
> 
>  --
>  ==**==
> 
>  Justin A. Lemkul, Ph.D.
>  Research Scientist
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
>  http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>  ==**==
>  --
>  gmx-users mailing listgmx-users@gromacs.org
>  http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>  * Please search the archive at http://www.gromacs.org/**
>  Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>  * Please don't post (un)subscribe requests to the list. Use the www
>  interface or send it to gmx-users-requ...@gromacs.org.
>  * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> 
> >>>
> >>>
> >> --
> >> ==**==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>
> >> ==**==
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
> http://www.gromacs.or

Re: [gmx-users] local pressure

2013-05-01 Thread XAvier Periole



Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are :)).

The paper related to the use would be: 
Ollila et al, PRL 102, 078101 (2009)
Ollila et al, Biophysical Journal (100)1651–59

On May 1, 2013, at 5:48 PM, Sikandar Mashayak  wrote:

> Thanks Xavier
> 
> 
> Can you please elaborate on how to use and post-process the local pressure
> version of gromacs? Do you have any examples or reference article?
> 
> May be you can create a HowTo wiki as Justin suggested, it would be of
> great help.
> 
> Thanks
> Sikandar
> 
> 
> On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul  wrote:
> 
>> 
>> 
>> On 5/1/13 5:12 AM, XAvier Periole wrote:
>> 
>>> 
>>> The use of the original code is quite straightforward, the post
>>> processing is a bit more confusing but quite accessible.
>>> 
>>> 
>> That would be a great topic for a wiki How-To.
>> 
>> 
>> We have been using this code (the one available on the site) and related
>>> version in the lab and we definitely would find it very sad to not keep
>>> this feature available in GROMACS.
>>> 
>>> 
>> I never said it would go away, but given the fact that there have been no
>> updates to the git branch in over 3 years, it's simply unlikely that anyone
>> has cared to move it forward.  If someone wants to update the code to be
>> compatible with 4.6, that would be a welcome contribution.  Lack of any
>> request for improvements and inclusion in an official release has likely
>> led to the decline in interest from the development team.  If you want
>> something included, you should file a feature request on
>> redmine.gromacs.org - it's the only official way we keep track of fixes
>> and features.  If it's not there, it likely won't get addressed until one
>> of the developers has a compelling need to work on it.
>> 
>> -Justin
>> 
>> 
>> On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:
>>> 
>>> 
 
 On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
 
> Hi
> 
> I found the branch of gromacs code called localpressure-4.0 at
> http://redmine.gromacs.org/**projects/gromacs/repository/**
> show?rev=localpressure-4-0
> .
> I am wondering whether this code can compute the spatial variation of
> pressure in given system. And if it does, how stable is this branch? Are
> there any known issues with it? And any particular reason this is not
> included in main gromacs releases?
> 
> 
 Lack of documentation has made it very difficult to use, it is extremely
 slow, and no one ever asks about it except once every few years.  All of
 those factors make it unlikely to ever incorporate into an actual release.
 Given that the development process has gone on for years in the absence of
 any real interest in the localpressure branch, it's probably more trouble
 than it's worth to get it up and running effectively.
 
 -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
 
>>> 
>>> 
>> --
>> ==**==
>> 
>> 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
>> 
> -- 
> gmx-users mailing listgmx

Re: [gmx-users] local pressure

2013-05-01 Thread Sikandar Mashayak

Thanks Xavier


Can you please elaborate on how to use and post-process the local pressure
version of gromacs? Do you have any examples or reference article?

May be you can create a HowTo wiki as Justin suggested, it would be of
great help.

Thanks
Sikandar


On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul  wrote:

>
>
> On 5/1/13 5:12 AM, XAvier Periole wrote:
>
>>
>> The use of the original code is quite straightforward, the post
>> processing is a bit more confusing but quite accessible.
>>
>>
> That would be a great topic for a wiki How-To.
>
>
>  We have been using this code (the one available on the site) and related
>> version in the lab and we definitely would find it very sad to not keep
>> this feature available in GROMACS.
>>
>>
> I never said it would go away, but given the fact that there have been no
> updates to the git branch in over 3 years, it's simply unlikely that anyone
> has cared to move it forward.  If someone wants to update the code to be
> compatible with 4.6, that would be a welcome contribution.  Lack of any
> request for improvements and inclusion in an official release has likely
> led to the decline in interest from the development team.  If you want
> something included, you should file a feature request on
> redmine.gromacs.org - it's the only official way we keep track of fixes
> and features.  If it's not there, it likely won't get addressed until one
> of the developers has a compelling need to work on it.
>
> -Justin
>
>
>  On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
>>>
 Hi

 I found the branch of gromacs code called localpressure-4.0 at
 http://redmine.gromacs.org/**projects/gromacs/repository/**
 show?rev=localpressure-4-0
 .
 I am wondering whether this code can compute the spatial variation of
 pressure in given system. And if it does, how stable is this branch? Are
 there any known issues with it? And any particular reason this is not
 included in main gromacs releases?


>>> Lack of documentation has made it very difficult to use, it is extremely
>>> slow, and no one ever asks about it except once every few years.  All of
>>> those factors make it unlikely to ever incorporate into an actual release.
>>>  Given that the development process has gone on for years in the absence of
>>> any real interest in the localpressure branch, it's probably more trouble
>>> than it's worth to get it up and running effectively.
>>>
>>> -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
>>>
>>
>>
> --
> ==**==
>
> 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
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] stable branch using git

2013-05-01 Thread Sikandar Mashayak

Thanks Justin and Mark

I think I would checkout and create a branch from v4.6 tag.

One more thing, would it be an issue if I install mulitple
version's/branche's binaries and libraries in the same folder with branch
specific suffixes to distinguish between them?

Thanks
Sikandar


On Wed, May 1, 2013 at 3:25 AM, Mark Abraham wrote:

> On Wed, May 1, 2013 at 2:50 AM, Sikandar Mashayak  >wrote:
>
> > Hi Justin
> >
> > Thanks for explanation. But I am a bit confused because I am new to git.
> > When I check out release-4-6 branch, the source code should be the same
> as
> > the one in tarball from Gromacs website, right?
>
>
> No. The tarball is made from a particular commit and that commit has a git
> tag identifying it (though I did mess that up slightly for 4.6.1). History
> then continues in the branch. Its head commit only coincides with a tag
> immediately after a release.
>
>
> > When I run git status I get
> > # On branch release-4-6
> > nothing to commit (working directory clean), I believe that means I have
> > the released version of the code.
> >
>
> No, you have the head of the development branch from which releases are
> currently being made. Do check out some git tutorial material.
>
> The reason I am doing this is that I want to have just one directory for
> > gromacs with subdirectories for its src, build and binaries. And in
> future,
> > instead of downloading new releases, I want to just pull the changes and
> > re-build.
>
>
> In principle, that workflow can work, but you need to (e.g.) use "git
> checkout v4.6" to check out the commit we tagged when we built the 4.6
> tarball.
>
>
> > Also, I plan to clone the same src directory on my different
> > machines, so that I can have the same version on all machines.
>
>
> You can do similar things with the tarball, so I don't see what you're
> gaining :-)
>
> Mark
>
> Hopefully,
> > in the future I may start doing some modifications here n there.
> >
> > Thanks
> > Sikandar
> >
> >
> > On Tue, Apr 30, 2013 at 7:38 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 4/30/13 8:28 PM, Sikandar Mashayak wrote:
> > >
> > >> Thanks Justin.
> > >>
> > >> I replaced release-4-5-patches with release-4-6 while checking out the
> > >> branch.
> > >> When I installed it and checked the version string I get VERSION
> > >> 4.6.2-dev-20130429-d13fc48.
> > >> Does that mean I got the version which is still under development and
> > not
> > >> stable and tested?
> > >> Should I be concerned using it to do a production run?
> > >>
> > >>
> > > We generally discourage anyone from doing production work with anything
> > > that's not an official release.  Anything you pull from the git repo
> is a
> > > work in progress.  Periodic releases are generated when the code is
> > > believed to be production-ready.  We do code review and build testing
> and
> > > each patch is as reliable as we believe it to be :)
> > >
> > > The reference to a "stable branch" is probably a bit misleading, but
> the
> > > master branch is currently undergoing large-scale changes, leaving it
> > > perhaps a bit more "unstable" than release-4-6.  The release-4-6 branch
> > is
> > > the one from which the development team is producing actual releases.
> > >
> > > If you want the latest version, just download the 4.6.1 tarball from
> the
> > > Gromacs website.  Version 4.6.2 should be out fairly soon, but there
> are
> > > some issues that are still being cleaned up.
> > >
> > >
> > > -Justin
> > >
> > > --
> > > ==**==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >
> > > ==**==
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > * Please search the archive at http://www.gromacs.org/**
> > > Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http:

[gmx-users] minimization of particular residue/atom

2013-05-01 Thread gromacs query

Dear All,

I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.

Potential Energy  =  4.6809051e+19
Maximum force =inf on atom 4281
Norm of force =inf


(inf means? means infinite/NAN)

I removed the  full lipid residue having atom number 4281. I was again
getting error representing some other atoms so finally I removed three
lipid residues. Doing this I was able to complete convergence.

I have two queries:

1) As I have removed three residues from Charmm gui membrane, does this
affect final results? Although I will be doing MD for membrane first.

2) Also is there any way so that particular atoms can be minimized or
''touched'' ? Here in this case I removed three lipid residues but this
will not be good say in case of proteins. Just as a analogy if this problem
arises  in AMBER (rather I faced such problem many times) I can use xleap
and can move atom a little and relax it particularly by selecting it , so
that later if use the edited structure I get convergence properly without
error.

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

Re: [gmx-users] Re: Using virtual site

2013-05-01 Thread Richard Broadbent


Dear Raju,

You haven't added any exclusions to your topology. Therefore, the mid 
point is interacting via the coulomb potential with the Carbon and 
Oxygen atoms.


If you exclude those interactions this system will probably run.

Richard

On 01/05/13 14:16, 라지브간디 wrote:

Dear
Mark,




As per you suggestion, I have simulated a single CO as well as
CO-with-vsite in a box.




A single CO runs without any problem, BUT the CO-with-vsite
gives an same error as before:




Steepest
Descents:

Tolerance (Fmax)   =
  1.0e+03

Number of steps=
  5

Step=0, Dmax= 1.0e-02 nm, Epot=
-3.73341e+04 Fmax= 3.38911e+05, atom= 2

Step=1, Dmax= 1.0e-02 nm, Epot=
-4.54970e+04 Fmax= 4.95889e+05, atom= 2

Step=2, Dmax= 1.2e-02 nm, Epot=
-6.18180e+04 Fmax= 9.34585e+05, atom= 2

Step=3, Dmax= 1.4e-02 nm, Epot=
-1.10395e+05 Fmax= 3.03088e+06, atom= 1

Step=5, Dmax= 8.6e-03 nm, Epot=
-2.09874e+05 Fmax= 1.09138e+07, atom= 2

Step=9, Dmax= 1.3e-03 nm, Epot=
-2.42526e+05 Fmax= 1.45550e+07, atom= 1

Step=   11, Dmax= 7.8e-04 nm, Epot=
-2.67493e+05 Fmax= 1.76910e+07, atom= 2

Step=   14, Dmax= 2.3e-04 nm, Epot=
-2.76005e+05 Fmax= 1.88299e+07, atom= 2

Step=   16, Dmax= 1.4e-04 nm, Epot=
-2.81365e+05 Fmax= 1.95651e+07, atom= 2

Step=   19, Dmax= 4.2e-05 nm, Epot=
-2.83032e+05 Fmax= 1.97967e+07, atom= 1

Step=   23, Dmax= 6.3e-06 nm, Epot=
-2.83281e+05 Fmax= 1.98315e+07, atom= 1

Step=   26, Dmax= 1.9e-06 nm, Epot=
-2.83355e+05 Fmax= 1.98418e+07, atom= 2

Step=   28, Dmax= 1.1e-06 nm, Epot=
nan Fmax= 0.0e+00, atom= 0

Stepsize too small, or no change in energy.

Converged to machine precision,

but not to the requested precision Fmax < 1000




Double precision normally gives you higher
accuracy.




writing lowest energy coordinates.




Back Off! I just backed up min.gro to ./#min.gro.1#




Steepest Descents converged to machine precision in
29 steps,

but did not reach the requested Fmax < 1000.

Potential Energy  = -2.8335531e+05

Maximum force =  1.9841798e+07
on atom 2

Norm of force =  1.6200760e+07







I am afraid that I am a making any mistakes of setting the
vsite?





My
topology file vsite setting :




[ moleculetype ]


;
Namenrexcl

Other_chain_A   3



[ atoms ]

;   nr   type  resnr
residue  atom   cgnr charge   mass
  typeBchargeB  massB

; residue 157 CMO rtp CMO  q -1.6

  1
  C157CMO  C
  1  -0.75 12.011   ; qtot -0.75

  2
  O157CMO  O
  2  -0.8515.9994   ; qtot -1.6

  3
  I 157 CMO  I
   3   1.6  0.

[ bonds ]

;  aiaj funct
c0c1
c2
  c3

 1 2 2
gb_4

[ virtual_sites2 ]

; Vsite fromfunct
   a




3   1 2
 1   0.4376625







My coordiante (.gro) file where i added the vsite xyz: Also included
the vsite atom info in atomypes as well as ffnonbonded.itp.




Gravel
Rubs Often Many Awfully Cauterized Sores


   3


157CMO  C1   1.625   2.697
0.490


157CMO  O2   1.722   2.647
0.482


157CMO   I 3   1.673   2.672
   0.486

  0.09660
   0.05040   0.00760

~






Could you tell what mistakes I am making here ?





Thanks in advance.





Raju





On Wed, May 1, 2013 at ��� :



I mean simulate a single CO in a box. Then CO-with-vsite in a box.
If you
can do that, then a bunch of problems are known to be solved. Leaping in
the deep end with a complex system means you don't know where the trouble
comes from when you have it.

Mark

On Wed, May 1, 2013 at 8:45 AM, ���
 wrote:


Dear Mark,


You mean do the CO simulation and then add V-site upon

production run?


Could you please more specific, what has to be done to avoid this

error?


  >
On Fri, Apr 26, 2013 at 6:16 PM, ��

 wrote:


Maybe your starting configuration of atoms is too broken to be

useful.

Maybe you have some interaction on atom 2513 that doesn't work.

Make a simple system of CO work, then do CO+vsite. Then apply those

lessons

to your complex system.

Mark








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

[gmx-users] Re: Using virtual site

2013-05-01 Thread 라지브간디

Dear
Mark, 

 


As per you suggestion, I have simulated a single CO as well as
CO-with-vsite in a box.

 


A single CO runs without any problem, BUT the CO-with-vsite
gives an same error as before:

 


Steepest
Descents:

   Tolerance (Fmax)   =
 1.0e+03

   Number of steps=  
 5

Step=0, Dmax= 1.0e-02 nm, Epot=
-3.73341e+04 Fmax= 3.38911e+05, atom= 2

Step=1, Dmax= 1.0e-02 nm, Epot=
-4.54970e+04 Fmax= 4.95889e+05, atom= 2

Step=2, Dmax= 1.2e-02 nm, Epot=
-6.18180e+04 Fmax= 9.34585e+05, atom= 2

Step=3, Dmax= 1.4e-02 nm, Epot=
-1.10395e+05 Fmax= 3.03088e+06, atom= 1

Step=5, Dmax= 8.6e-03 nm, Epot=
-2.09874e+05 Fmax= 1.09138e+07, atom= 2

Step=9, Dmax= 1.3e-03 nm, Epot=
-2.42526e+05 Fmax= 1.45550e+07, atom= 1

Step=   11, Dmax= 7.8e-04 nm, Epot=
-2.67493e+05 Fmax= 1.76910e+07, atom= 2

Step=   14, Dmax= 2.3e-04 nm, Epot=
-2.76005e+05 Fmax= 1.88299e+07, atom= 2

Step=   16, Dmax= 1.4e-04 nm, Epot=
-2.81365e+05 Fmax= 1.95651e+07, atom= 2

Step=   19, Dmax= 4.2e-05 nm, Epot=
-2.83032e+05 Fmax= 1.97967e+07, atom= 1

Step=   23, Dmax= 6.3e-06 nm, Epot=
-2.83281e+05 Fmax= 1.98315e+07, atom= 1

Step=   26, Dmax= 1.9e-06 nm, Epot=
-2.83355e+05 Fmax= 1.98418e+07, atom= 2

Step=   28, Dmax= 1.1e-06 nm, Epot=  
   nan Fmax= 0.0e+00, atom= 0

Stepsize too small, or no change in energy.

Converged to machine precision,

but not to the requested precision Fmax < 1000

 


Double precision normally gives you higher
accuracy.

 


writing lowest energy coordinates.

 


Back Off! I just backed up min.gro to ./#min.gro.1#

 


Steepest Descents converged to machine precision in
29 steps,

but did not reach the requested Fmax < 1000.

Potential Energy  = -2.8335531e+05

Maximum force =  1.9841798e+07
on atom 2

Norm of force =  1.6200760e+07

 


 


I am afraid that I am a making any mistakes of setting the
vsite? 


 


My
topology file vsite setting :

 


[ moleculetype ]


;
Namenrexcl 

Other_chain_A   3



[ atoms ]

;   nr   type  resnr
residue  atom   cgnr charge   mass
 typeBchargeB  massB

; residue 157 CMO rtp CMO  q -1.6

 1
 C157CMO  C
 1  -0.75 12.011   ; qtot -0.75

 2
 O157CMO  O
 2  -0.8515.9994   ; qtot -1.6

 3
 I 157 CMO  I
  3   1.6  0.

[ bonds ]

;  aiaj funct
   c0c1
   c2  
 c3

1 2 2
   gb_4

[ virtual_sites2 ]

; Vsite fromfunct
  a 

 


3   1 2 
1   0.4376625

 


 


My coordiante (.gro) file where i added the vsite xyz: Also included
the vsite atom info in atomypes as well as ffnonbonded.itp.

 


Gravel
Rubs Often Many Awfully Cauterized Sores

 
  3

 
157CMO  C1   1.625   2.697  
0.490

 
157CMO  O2   1.722   2.647  
0.482

 
157CMO   I 3   1.673   2.672
  0.486

 0.09660
  0.05040   0.00760

~
 


 


Could you tell what mistakes I am making here ?


 


Thanks in advance.


 


Raju

 

 

On Wed, May 1, 2013 at ��� :



I mean simulate a single CO in a box. Then CO-with-vsite in a box.
If you 
can do that, then a bunch of problems are known to be solved. Leaping in 
the deep end with a complex system means you don't know where the trouble 
comes from when you have it. 

Mark 

On Wed, May 1, 2013 at 8:45 AM, ���
 wrote: 

> Dear Mark, 
> 
> > You mean do the CO simulation and then add V-site upon
production run? 
> 
> Could you please more specific, what has to be done to avoid this
error? 
> 
>  > 
> On Fri, Apr 26, 2013 at 6:16 PM, ��
 wrote: 
> 
> Maybe your starting configuration of atoms is too broken to be
useful. 
> Maybe you have some interaction on atom 2513 that doesn't work. 
> 
> Make a simple system of CO work, then do CO+vsite. Then apply those
lessons 
> to your complex system. 
> 
> Mark 
> 

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

RE: [gmx-users] help with g_hydorder and g_polystat

2013-05-01 Thread Emmanuel, Alaina


No, using a trajectory file with g_hydorder hasn't made any difference. The 
error is still the same.

When I use g_polystat, I use the following command: 

g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg 
-o polystat.xvg

Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than 
using the whole polymer structure in an index file. 

Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 01 May 2013 10:58
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 9:00 PM, Emmanuel, Alaina wrote:
> Hello Justin,
>
> My mdp file shows that the pbc was set to xyz.
>

Instead of analyzing a coordinate file, does it work with a trajectory?
Regarding g_polystat and the nan's, what command are you issuing?

-Justin

>
> Kind Regards,
>
> Alaina
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin Lemkul [jalem...@vt.edu]
> Sent: 30 April 2013 16:10
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] help with g_hydorder and g_polystat
>
> On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
>> Dear All,
>>
>> I'm fairly new to gromacs and having a bit of problem with the g_hydorder 
>> and g_polystat. Thanks in advanced for your time.
>>
>> For g_hydorder,
>> I get a fatal error when I type the following command:
>> g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
>> Error:
>> Internal error in pbc_dx, set pbc has nor been called
>> For more information..
>> 
>>
>> I'm not sure what this means. It seems to be implying that I don't have a 
>> box around my polymer, but the gro file clearly shows that my box is 4.94 x 
>> 4.94 x 4.94. Any ideas?
>>
>
> What is your setting for the pbc keyword in the .mdp file?
>
>>
>> For g_polystat, I'm a bit worried about the persistence lengths that I get 
>> for short polymers. With repeat units smaller than 50 these usually show 
>> "nan" values, that cannot be plotted. From reading the gmx threads I've 
>> found that Nan stands for "Not a Number", but why do these "nan" values 
>> appear and how can I prevent it so that I can read in my results?
>>
>
> This could be an underlying problem related to the above interpretation of
> periodicity.  We don't have enough information to say for sure yet.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

--


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


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


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

[gmx-users] g_msd for many molecules

2013-05-01 Thread George Patargias

Hello

I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
g_msd. If I include the atoms of all these 8 molecules as a single group
in the index file, will g_msd calculate the MSD of the center of mass of
them or it will average over all atoms?


Thanks
George


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

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

2013-05-01 Thread Reza Salari

Hi Justin,

I actually did :) but it ended up being bigger than 50 kb so it needed
moderator approval to show up. I was hoping it would've been released by
now. I'll attach a the details below.

Any help/hint is highly appreciated.

Reza

Details:

*1)* Both systems were prepared using VMD "membrane" package and then
waters were removed. I used Gromacs 4.6.1 and NAMD 2.9.

*2)* Simulations were run in vacuum as a single-point energy calculations
(0 step). PME was not used.

*3) *For Gromacs runs, pdb2gmx was used to prepare the system and the
output was saved as the pdb format. The mdp file:

integrator= md
nsteps= 0
nstlog  = 1
nstlist= 1
ns_type= grid
rlist= 100.0
coulombtype= cut-off
rcoulomb= 100.0
rvdw= 100.0
pbc = no

*4) *NAMD input file:

structure  ../0_prep/memb_nowat.psf
paratypecharmm  on
parameterspar_all27_prot_lipid.prm
exclude scaled1-4
1-4scaling 1.0
switching off
switchdist 8
cutoff 1000
pairlistdist 1000
margin 0
timestep 1.0
outputenergies 1
outputtiming 1
binaryoutput no
coordinates ../0_prep/memb_nowat.pdb
outputname out
dcdfreq 10
temperature 300
run 0

*5)* Energies:

For Single POPC  (kcal/mol)


Gromacs NAMD Diff

Bond 43.0022 43.0015 -0.0007
Angle 80.6568 80.6571 0.0003
Dih 29.8083 29.8083 0.
Imp 0.8452 0.8452 0.

Coul -17.2983 -17.2983 0.
LJ -7.0798 -7.0798 0.

Pot 129.9343 129.9340 -0.0003



For POPC Memb (kcal/mol)

Gromacs NAMD Diff

Bond 1539.1181 1539.1162 -0.0019
Angle 3111.9264 3111.9197 -0.0067
Dih 1250.5425 1250.5421 -0.0004
Imp 16.2837 16.2837 0.

Coul -1837.8585 -1705.3075 132.5510
LJ -995.0311   -1219.3432 -224.3121

Pot 3084.9904 2993.2110 -91.7794





On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul  wrote:

>
>
> On 4/30/13 4:19 PM, Reza Salari wrote:
>
>> Hi
>>
>> I have set up two small systems, one with a single POPC lipid, and another
>> system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
>> similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting
>> charmm ff to gromacs) for my systems. My main question is that for the
>> single POPC, all the potential energy terms match very well, but for the
>> membrane system the non-bonding terms differ significantly.
>>
>> I am providing the full details below and greatly appreciate any hint for
>> better comparison of the energies.
>>
>>
>> Thanks,
>> Reza Salari
>>
>> Details:
>>
>> 1) Both systems were prepared using VMD "membrane" package:
>>
>> 2)
>>
>>
> It appears you hit "send" too early.  Please provide the entirety of the
> details you intended.  Complete .mdp files and actual quantification of the
> differences you are observing are also very important.
>
> -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
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] local pressure

2013-05-01 Thread Justin Lemkul




On 5/1/13 5:12 AM, XAvier Periole wrote:


The use of the original code is quite straightforward, the post processing is a 
bit more confusing but quite accessible.



That would be a great topic for a wiki How-To.


We have been using this code (the one available on the site) and related 
version in the lab and we definitely would find it very sad to not keep this 
feature available in GROMACS.



I never said it would go away, but given the fact that there have been no 
updates to the git branch in over 3 years, it's simply unlikely that anyone has 
cared to move it forward.  If someone wants to update the code to be compatible 
with 4.6, that would be a welcome contribution.  Lack of any request for 
improvements and inclusion in an official release has likely led to the decline 
in interest from the development team.  If you want something included, you 
should file a feature request on redmine.gromacs.org - it's the only official 
way we keep track of fixes and features.  If it's not there, it likely won't get 
addressed until one of the developers has a compelling need to work on it.


-Justin


On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:




On 4/30/13 8:01 PM, Sikandar Mashayak wrote:

Hi

I found the branch of gromacs code called localpressure-4.0 at
http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0.
I am wondering whether this code can compute the spatial variation of
pressure in given system. And if it does, how stable is this branch? Are
there any known issues with it? And any particular reason this is not
included in main gromacs releases?



Lack of documentation has made it very difficult to use, it is extremely slow, 
and no one ever asks about it except once every few years.  All of those 
factors make it unlikely to ever incorporate into an actual release.  Given 
that the development process has gone on for years in the absence of any real 
interest in the localpressure branch, it's probably more trouble than it's 
worth to get it up and running effectively.

-Justin

--


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


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




--


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


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

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

Re: [gmx-users] input file for umbrella sampling

2013-05-01 Thread Justin Lemkul




On 5/1/13 12:58 AM, Arunima Shilpi wrote:

hi alll
  How to generate input.pdb file for umbrella sampling.




As I told you yesterday 
(http://lists.gromacs.org/pipermail/gmx-users/2013-April/080834.html), please 
don't reply to a digest, and if you're starting a new thread, give it an 
informative title.  If you want people to help you, you have to make it easy to 
do so and clear what you are doing.


Your question cannot be answered.  You need to state what you are working with 
and what your objective is.


-Justin

--


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


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

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

Re: [gmx-users] help with g_hydorder and g_polystat

2013-05-01 Thread Justin Lemkul




On 4/30/13 9:00 PM, Emmanuel, Alaina wrote:

Hello Justin,

My mdp file shows that the pbc was set to xyz.



Instead of analyzing a coordinate file, does it work with a trajectory? 
Regarding g_polystat and the nan's, what command are you issuing?


-Justin



Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:

Dear All,

I'm fairly new to gromacs and having a bit of problem with the g_hydorder and 
g_polystat. Thanks in advanced for your time.

For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
Error:
Internal error in pbc_dx, set pbc has nor been called
For more information..


I'm not sure what this means. It seems to be implying that I don't have a box 
around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 
4.94. Any ideas?



What is your setting for the pbc keyword in the .mdp file?



For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat 
units smaller than 50 these usually show "nan" values, that cannot be plotted. From reading the gmx 
threads I've found that Nan stands for "Not a Number", but why do these "nan" values 
appear and how can I prevent it so that I can read in my results?



This could be an underlying problem related to the above interpretation of
periodicity.  We don't have enough information to say for sure yet.

-Justin

--


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


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




--


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


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

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

Re: [gmx-users] local pressure

2013-05-01 Thread XAvier Periole


The use of the original code is quite straightforward, the post processing is a 
bit more confusing but quite accessible. 

We have been using this code (the one available on the site) and related 
version in the lab and we definitely would find it very sad to not keep this 
feature available in GROMACS.

On May 1, 2013, at 2:34 AM, Justin Lemkul  wrote:

> 
> 
> On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
>> Hi
>> 
>> I found the branch of gromacs code called localpressure-4.0 at
>> http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0.
>> I am wondering whether this code can compute the spatial variation of
>> pressure in given system. And if it does, how stable is this branch? Are
>> there any known issues with it? And any particular reason this is not
>> included in main gromacs releases?
>> 
> 
> Lack of documentation has made it very difficult to use, it is extremely 
> slow, and no one ever asks about it except once every few years.  All of 
> those factors make it unlikely to ever incorporate into an actual release.  
> Given that the development process has gone on for years in the absence of 
> any real interest in the localpressure branch, it's probably more trouble 
> than it's worth to get it up and running effectively.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

Re: [gmx-users] Re:Using virtual site

2013-05-01 Thread Mark Abraham

I mean simulate a single CO in a box. Then CO-with-vsite in a box. If you
can do that, then a bunch of problems are known to be solved. Leaping in
the deep end with a complex system means you don't know where the trouble
comes from when you have it.

Mark


On Wed, May 1, 2013 at 8:45 AM, 라지브간디  wrote:

> Dear Mark,
>
>
> You mean do the CO simulation and then add V-site upon production run?
>
>
>
>
> Could you please more specific, what has to be done to avoid this error?
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Fri, Apr 26, 2013 at 6:16 PM, ��  wrote:
>
>
>
>
> Maybe your starting configuration of atoms is too broken to be useful.
> Maybe you have some interaction on atom 2513 that doesn't work.
>
> Make a simple system of CO work, then do CO+vsite. Then apply those lessons
> to your complex system.
>
> Mark
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] stable branch using git

2013-05-01 Thread Mark Abraham

On Wed, May 1, 2013 at 2:50 AM, Sikandar Mashayak wrote:

> Hi Justin
>
> Thanks for explanation. But I am a bit confused because I am new to git.
> When I check out release-4-6 branch, the source code should be the same as
> the one in tarball from Gromacs website, right?


No. The tarball is made from a particular commit and that commit has a git
tag identifying it (though I did mess that up slightly for 4.6.1). History
then continues in the branch. Its head commit only coincides with a tag
immediately after a release.


> When I run git status I get
> # On branch release-4-6
> nothing to commit (working directory clean), I believe that means I have
> the released version of the code.
>

No, you have the head of the development branch from which releases are
currently being made. Do check out some git tutorial material.

The reason I am doing this is that I want to have just one directory for
> gromacs with subdirectories for its src, build and binaries. And in future,
> instead of downloading new releases, I want to just pull the changes and
> re-build.


In principle, that workflow can work, but you need to (e.g.) use "git
checkout v4.6" to check out the commit we tagged when we built the 4.6
tarball.


> Also, I plan to clone the same src directory on my different
> machines, so that I can have the same version on all machines.


You can do similar things with the tarball, so I don't see what you're
gaining :-)

Mark

Hopefully,
> in the future I may start doing some modifications here n there.
>
> Thanks
> Sikandar
>
>
> On Tue, Apr 30, 2013 at 7:38 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/30/13 8:28 PM, Sikandar Mashayak wrote:
> >
> >> Thanks Justin.
> >>
> >> I replaced release-4-5-patches with release-4-6 while checking out the
> >> branch.
> >> When I installed it and checked the version string I get VERSION
> >> 4.6.2-dev-20130429-d13fc48.
> >> Does that mean I got the version which is still under development and
> not
> >> stable and tested?
> >> Should I be concerned using it to do a production run?
> >>
> >>
> > We generally discourage anyone from doing production work with anything
> > that's not an official release.  Anything you pull from the git repo is a
> > work in progress.  Periodic releases are generated when the code is
> > believed to be production-ready.  We do code review and build testing and
> > each patch is as reliable as we believe it to be :)
> >
> > The reference to a "stable branch" is probably a bit misleading, but the
> > master branch is currently undergoing large-scale changes, leaving it
> > perhaps a bit more "unstable" than release-4-6.  The release-4-6 branch
> is
> > the one from which the development team is producing actual releases.
> >
> > If you want the latest version, just download the 4.6.1 tarball from the
> > Gromacs website.  Version 4.6.2 should be out fairly soon, but there are
> > some issues that are still being cleaned up.
> >
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] doubt in mdrun

2013-05-01 Thread Pablo Englebienne


Hi Shine,

The amount of data is due to a very long simulation (1 microsecond!) 
coupled to a very frequent dumping of snapshots (every 1000 frames).


You should question whether you need such frequent storage of the 
trajectory (e.g., for analysis of diffusion) or if less frequent will do 
just fine. Also, question whether you need such a long simulation or a 
shorter one would be sufficient.


In any case, you could do a shorter run, analyze the trajectory and 
continue the simulation as described in 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations .


Cheers,
Pablo

Dr. Pablo Englebienne
Postdoctoral Researcher

*TU Delft / 3mE / Process & Energy*
/Engineering Thermodynamics (ETh) group/

Building 46
Leeghwaterstraat 44, room 030
2628 CA Delft
The Netherlands

*T* +31 (0)15 27 86662 
*E* p.englebie...@tudelft.nl 

On 05/01/2013 07:29 AM, Shine A wrote:

Sir,

 I studying the dynamics of a peptide in explicit solvent model.But
during the mdrun I got the message like this.
NOTE 1 [file md.mdp]:
   This run will generate roughly 1177130 Mb of data
why the run generating this much amount of data?
The md.mdp file I used is shown below


title   = OPLS Lysozyme MD
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps, 1000 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstxtcout   = 1000  ; xtc compressed trajectory output every 2
ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation= yes   ; Restarting after NPT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 320   320 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar

compressibility = 4.5e-5; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off


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

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

Re: [gmx-users] local pressure

[gmx-users] Temperature for individual amino acid residues

[gmx-users] PMF calculation between protein and ligand

[gmx-users] surrounding a peptide by ions of magnesium

Re: [gmx-users] Gromacs mpi error while running REMD

[gmx-users] Gromacs mpi error while running REMD

Re: [gmx-users] g_msd for many molecules

Re: [gmx-users] g_msd for many molecules

Re: [gmx-users] help with g_hydorder and g_polystat

Re: [gmx-users] minimization of particular residue/atom

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Re: [gmx-users] Re: Using virtual site

Re: [gmx-users] stable branch using git

Re: [gmx-users] local pressure

Re: [gmx-users] issue in replica exchange

Re: [gmx-users] local pressure

Re: [gmx-users] local pressure

Re: [gmx-users] local pressure

Re: [gmx-users] stable branch using git

[gmx-users] minimization of particular residue/atom

Re: [gmx-users] Re: Using virtual site

[gmx-users] Re: Using virtual site

RE: [gmx-users] help with g_hydorder and g_polystat

[gmx-users] g_msd for many molecules

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Re: [gmx-users] local pressure

Re: [gmx-users] input file for umbrella sampling

Re: [gmx-users] help with g_hydorder and g_polystat

Re: [gmx-users] local pressure

Re: [gmx-users] Re:Using virtual site

Re: [gmx-users] stable branch using git

Re: [gmx-users] doubt in mdrun

32 matches

Site Navigation

Mail list logo

Footer information