[gmx-users] questions about umbrella sampling tutorial

[Albert]

Hello:

 I am trying to do umbrella sampling for a protein/ligand water system 
these days following Justin's nice tutorial. And I've got some questions:


(1) in the tutorial, the small peptide was pulling along Z direction. I 
am just wondering, will the small peptide be pulled in both +Z and -Z 
direction?


In my case I've got a ligand in the deep pocket, it is possible that the 
ligand can escape the binding pocket from two opposite site, let's say 
-Z and +Z which I hope the umbrella sampling can give me some evidences 
to prove this  Could the umbrella sampling answer this question? Or 
we should pull the ligand along X,Y and Z three direction so that it is 
more convinced?


(2) it is said that when doing free energy calculation in gromacs, we'db 
better use double precision Gromacs. So probably we have to use CPU 
instead of GPU for this?


thank you very much
best
Albert
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[gmx-users] HIS in charmm27.ff

[라지브간디]

Dear gmx,
I understood that CHARMM supports two neutral/protonated histidine (HSD/HSE) 
and fully protonated(HSP). How about the heme bound HIS version? I couldn't 
find the HIS1 which knows as histidine bound to a heme? how do i link the heme 
bound his using charmm27.ff.




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Re: [gmx-users] replica exchange data in cpt file

[João Henriques]

Thank you Mark and Francesco. I will be pleased to contribute with a fix in
case I come up with a fairly general solution for this issue.

Best regards,
João Henriques


On Thu, Apr 4, 2013 at 7:45 PM, Mark Abraham wrote:

> Demux.pl pre-dates .cpt and -append. The only solution is to preserve your
> .log files (e.g. with -noappend) and post-process. If you do that by
> modifying demux.pl, please consider contributing your fix back.
>
> Mark
> On Apr 4, 2013 1:42 PM, "francesco oteri" 
> wrote:
>
> > if your -append option is activated (the default is yes),
> > maybe Demux.pl reads the exchanging from the .log taking into account the
> > time in the
> > log and so you don't need to do anything.
> > But I don't know how Demux.pl works :(
> >
> > Francesco
> >
> > 2013/4/4 João Henriques 
> >
> > > That's terrible! I was just about to restart 2 hefty REMD
> simulations...
> > > Maybe I can move the original log files somewhere and combine them with
> > the
> > > restart ones afterwards by using a script. It's just an idea, because I
> > > need to run Demux.pl on the final concatenated log file.
> > >
> > > Any other issues I should be aware of?
> > >
> > > Best regards,
> > > João Henriques
> > >
> > >
> > > On Thu, Apr 4, 2013 at 12:18 PM, francesco oteri
> > > wrote:
> > >
> > > > This is what I meant,
> > > > in particular it is a problem when I want to analyze
> > > > the data regarding the exchange probability.
> > > >
> > > > Francesco
> > > >
> > > > 2013/4/4 João Henriques 
> > > >
> > > > > So let me see if I understood what Francesco said correctly.
> > > Restarting a
> > > > > REMD job after hitting the cluster wall-time limit resets the
> > > information
> > > > > stored in the log files? Can someone shed some light on this
> subject?
> > > > >
> > > > > Best regards,
> > > > > João Henriques
> > > > > --
> > > > > gmx-users mailing listgmx-users@gromacs.org
> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> posting!
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Cordiali saluti, Dr.Oteri Francesco
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > > >
> > >
> > >
> > >
> > > --
> > > João Henriques
> > > --
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> > >
> >
> >
> >
> > --
> > Cordiali saluti, Dr.Oteri Francesco
> > --
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-- 
João Henriques
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[gmx-users] Intel compiling failed

[Albert]

Hello:

 I am trying to compile gromacs with intel compiler. However, it failed 
when I compile FFTW3 with command:



./configure --enable-sse --enable-float --with-pic --enable-single 
--enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 
CC=icc CXX=icc F77=ifort


here is the log file:

mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset'
../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined 
references to `_intel_fast_memset' follow

collect2: ld returned 1 exit status
make[3]: *** [mpi-bench] Error 1
make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3'


make: *** [all] Error 2

thank you very much
best
Albert
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Re: [gmx-users] Intel compiling failed

[Carsten Kutzner]

Hi Albert,

one reason for the error you see could be that you are using a non-Intel
MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.

Carsten


On Apr 5, 2013, at 12:25 PM, Albert  wrote:

> Hello:
> 
> I am trying to compile gromacs with intel compiler. However, it failed when I 
> compile FFTW3 with command:
> 
> 
> ./configure --enable-sse --enable-float --with-pic --enable-single 
> --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc 
> CXX=icc F77=ifort
> 
> here is the log file:
> 
> mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset'
> ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references 
> to `_intel_fast_memset' follow
> collect2: ld returned 1 exit status
> make[3]: *** [mpi-bench] Error 1
> make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
> make[2]: *** [all] Error 2
> make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3'
> 
> 
> make: *** [all] Error 2
> 
> thank you very much
> best
> Albert
> -- 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] g_select: selection file problem

[Teemu Murtola]

Hi,

On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko
wrote:

> I'm want to analyse stratified layers of water around protein,
> so I provide next selection file to g_select:

[clip]
> (shell2 is supposed to be a layer of whole water molecules from the layer
> 3 to 4 A)
> but it doesn't work correctly, moreover it even provides different results
> when just changing
> the order in 3rd line (shell2 = shell1 and shell), which shouldn't be the
> case.
> Interestingly, 1st and 2nd line separately works correctly.
>
> Even more interesting the next selection file works perfectly fine
> (regardless the order in 3rd line):
> [clip]
>

Thanks for reporting this, this is clearly a bug. I have filed
http://redmine.gromacs.org/issues/1216 with some explanation of what
triggers the bug.

(this also provides a layer between 3 and 4 A from protein, but some
> molecules are represented only by 1 or 2 atoms, which I want to avoid,
> that's why I'm using 'same residue as')
>

There is probably no way to get exactly your condition before the bug is
fixed, but if you are OK with a slightly altered condition, you can do, for
example, this (haven't tested, but should work):

shell = group "SOL" and res_com within 0.4 of group "protein";
shell1 = group "SOL" and not res_com within 0.3 of group "protein";
shell2 = shell and shell1;
shell2;

Best regards,
Teemu
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Re: [gmx-users] Intel compiling failed

[Justin Lemkul]

On 4/5/13 6:38 AM, Carsten Kutzner wrote:

Hi Albert,

one reason for the error you see could be that you are using a non-Intel
MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.



Is there any point in compiling FFTW in parallel?  I have never once done it nor 
found it necessary.


-Justin


On Apr 5, 2013, at 12:25 PM, Albert  wrote:


Hello:

I am trying to compile gromacs with intel compiler. However, it failed when I 
compile FFTW3 with command:


./configure --enable-sse --enable-float --with-pic --enable-single 
--enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc 
CXX=icc F77=ifort

here is the log file:

mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset'
../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references 
to `_intel_fast_memset' follow
collect2: ld returned 1 exit status
make[3]: *** [mpi-bench] Error 1
make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3'


make: *** [all] Error 2

thank you very much
best
Albert
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa



--


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


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Re: [gmx-users] questions about umbrella sampling tutorial

[Justin Lemkul]

On 4/5/13 3:29 AM, Albert wrote:

Hello:

  I am trying to do umbrella sampling for a protein/ligand water system these
days following Justin's nice tutorial. And I've got some questions:

(1) in the tutorial, the small peptide was pulling along Z direction. I am just
wondering, will the small peptide be pulled in both +Z and -Z direction?

In my case I've got a ligand in the deep pocket, it is possible that the ligand
can escape the binding pocket from two opposite site, let's say -Z and +Z which
I hope the umbrella sampling can give me some evidences to prove this  Could
the umbrella sampling answer this question? Or we should pull the ligand along
X,Y and Z three direction so that it is more convinced?



The peptide is pulled/restrained in whatever direction you tell it.  The 
tutorial is just a simple example of the most trivial case, a one-dimensional 
pull along an axis.  You can do far more complex things using appropriate settings.



(2) it is said that when doing free energy calculation in gromacs, we'db better
use double precision Gromacs. So probably we have to use CPU instead of GPU for
this?



I don't think the pull code works on GPU (someone correct me if I'm wrong), but 
in any case, I think the general reference to "free energy calculations" usually 
just refers to alchemical transformations.  In most cases with umbrella 
sampling, your error bars will be orders of magnitude larger than any increase 
in precision.


-Justin

--


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


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Re: [gmx-users] HIS in charmm27.ff

[Justin Lemkul]

On 4/5/13 4:23 AM, 라지브간디 wrote:

Dear gmx,
I understood that CHARMM supports two neutral/protonated histidine (HSD/HSE) 
and fully protonated(HSP). How about the heme bound HIS version? I couldn't 
find the HIS1 which knows as histidine bound to a heme? how do i link the heme 
bound his using charmm27.ff.




It's not included by default, but suitable parameters probably exist in the 
literature, which makes it fairly easy to implement.


-Justin

--


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


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Re: [gmx-users] Intel compiling failed

[Carsten Kutzner]

On Apr 5, 2013, at 12:52 PM, Justin Lemkul  wrote:

> 
> 
> On 4/5/13 6:38 AM, Carsten Kutzner wrote:
>> Hi Albert,
>> 
>> one reason for the error you see could be that you are using a non-Intel
>> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
>> 
> 
> Is there any point in compiling FFTW in parallel?  I have never once done it 
> nor found it necessary.
Hi,

you are absolutely right, sorry I did not express that clearly. The thing is, 
if you
compile the FFTW using the Intel compiler and then compile Gromacs using Intels
mpicc or mpigcc compiler wrapper, you will get these undefined references to 
_intel*
at link time. To make it work, you need to use the mpiicc (two i's here) 
compiler wrapper
for Gromacs.

Carsten

> 
> -Justin
> 
>> On Apr 5, 2013, at 12:25 PM, Albert  wrote:
>> 
>>> Hello:
>>> 
>>> I am trying to compile gromacs with intel compiler. However, it failed when 
>>> I compile FFTW3 with command:
>>> 
>>> 
>>> ./configure --enable-sse --enable-float --with-pic --enable-single 
>>> --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 
>>> CC=icc CXX=icc F77=ifort
>>> 
>>> here is the log file:
>>> 
>>> mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset'
>>> ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined 
>>> references to `_intel_fast_memset' follow
>>> collect2: ld returned 1 exit status
>>> make[3]: *** [mpi-bench] Error 1
>>> make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
>>> make[2]: *** [all] Error 2
>>> make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3'
>>> 
>>> 
>>> make: *** [all] Error 2
>>> 
>>> thank you very much
>>> best
>>> Albert
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> 
>> 
>> --
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>> 
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] replica exchange data in cpt file

[Mark Abraham]

Great.

Some of the data at the end of the .log file is easily recomputed from
the output at every exchange attempt once the .log files are
concatenated, but there will be loss of precision in re-computing the
average exchange acceptance probability, etc.

Mark

On Fri, Apr 5, 2013 at 10:37 AM, João Henriques
 wrote:
> Thank you Mark and Francesco. I will be pleased to contribute with a fix in
> case I come up with a fairly general solution for this issue.
>
> Best regards,
> João Henriques
>
>
> On Thu, Apr 4, 2013 at 7:45 PM, Mark Abraham wrote:
>
>> Demux.pl pre-dates .cpt and -append. The only solution is to preserve your
>> .log files (e.g. with -noappend) and post-process. If you do that by
>> modifying demux.pl, please consider contributing your fix back.
>>
>> Mark
>> On Apr 4, 2013 1:42 PM, "francesco oteri" 
>> wrote:
>>
>> > if your -append option is activated (the default is yes),
>> > maybe Demux.pl reads the exchanging from the .log taking into account the
>> > time in the
>> > log and so you don't need to do anything.
>> > But I don't know how Demux.pl works :(
>> >
>> > Francesco
>> >
>> > 2013/4/4 João Henriques 
>> >
>> > > That's terrible! I was just about to restart 2 hefty REMD
>> simulations...
>> > > Maybe I can move the original log files somewhere and combine them with
>> > the
>> > > restart ones afterwards by using a script. It's just an idea, because I
>> > > need to run Demux.pl on the final concatenated log file.
>> > >
>> > > Any other issues I should be aware of?
>> > >
>> > > Best regards,
>> > > João Henriques
>> > >
>> > >
>> > > On Thu, Apr 4, 2013 at 12:18 PM, francesco oteri
>> > > wrote:
>> > >
>> > > > This is what I meant,
>> > > > in particular it is a problem when I want to analyze
>> > > > the data regarding the exchange probability.
>> > > >
>> > > > Francesco
>> > > >
>> > > > 2013/4/4 João Henriques 
>> > > >
>> > > > > So let me see if I understood what Francesco said correctly.
>> > > Restarting a
>> > > > > REMD job after hitting the cluster wall-time limit resets the
>> > > information
>> > > > > stored in the log files? Can someone shed some light on this
>> subject?
>> > > > >
>> > > > > Best regards,
>> > > > > João Henriques
>> > > > > --
>> > > > > 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
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Cordiali saluti, Dr.Oteri Francesco
>> > > > --
>> > > > 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
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > João Henriques
>> > > --
>> > > 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
>> > >
>> >
>> >
>> >
>> > --
>> > Cordiali saluti, Dr.Oteri Francesco
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> >
>> --
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>
>
>
> --
> João Henriques
> --
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[gmx-users] Re: g_select: selection file problem

[Oleksandr Sushko]

Teemu Murtola-3 wrote
> Hi,
> 
> On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko
> <

> o.sushko@.ac

> >wrote:
> 
>> I'm want to analyse stratified layers of water around protein,
>> so I provide next selection file to g_select:
> 
> [clip]
>> (shell2 is supposed to be a layer of whole water molecules from the layer
>> 3 to 4 A)
>> but it doesn't work correctly, moreover it even provides different
>> results
>> when just changing
>> the order in 3rd line (shell2 = shell1 and shell), which shouldn't be the
>> case.
>> Interestingly, 1st and 2nd line separately works correctly.
>>
>> Even more interesting the next selection file works perfectly fine
>> (regardless the order in 3rd line):
>> [clip]
>>
> 
> Thanks for reporting this, this is clearly a bug. I have filed
> http://redmine.gromacs.org/issues/1216 with some explanation of what
> triggers the bug.
> 
> (this also provides a layer between 3 and 4 A from protein, but some
>> molecules are represented only by 1 or 2 atoms, which I want to avoid,
>> that's why I'm using 'same residue as')
>>
> 
> There is probably no way to get exactly your condition before the bug is
> fixed, but if you are OK with a slightly altered condition, you can do,
> for
> example, this (haven't tested, but should work):
> 
> shell = group "SOL" and res_com within 0.4 of group "protein";
> shell1 = group "SOL" and not res_com within 0.3 of group "protein";
> shell2 = shell and shell1;
> shell2;
> 
> Best regards,
> Teemu
> -- 
> gmx-users mailing list

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your suggestion with res_com works fine,
although it results in less molecules for same shell compared to 'same
residue as',
but still keeps whole molecules in selection, which suits me.
thanks a lot,
Oleksandr



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Aw: [gmx-users] Re:Concept

[lloyd riggs]

 
So last week I read a post about liquid/gas layers in a box and it has me thinking (ie I cant shut it off).  As it would sim wise (and I asume there is already something somewhere that does it) for a large body of fileds such as astrophysics, liquid dynamics, gas/gas interface I woundered if anyone had thoughts on the subject.

 

It was pointed a standard box, say 200 nm cubed with half liquid, half gas or vacum quickly just diffuses the molecules across the area.  My thoughts were you could introduce a wall, with a set filed parameter in the mid point which would correct for some of the things happening.  I think now, a box would also have to be irregular for such things, ie 200x200x2000 or some extreem deminsion in one axis.  The point would be to do expirements say where I have a set atmosphere of several gases at a given pressure, etc...then introduce a solvent to half the box, ie just h2o, and then simulate the changes to this system in general to a final equilibrated point.  The main feature say I take 4 gases, CO2, NH3, O2, N2, and Ar or Ne, etc... The varied solubility of these is something like 3.5 g/L, 5 g/L , 0.02 g/L, etc... thus drastic effects on the atmospheric side of the box.  The delima is at the molecular level, there is a gas/liquid interface that in the real world is not to pretty to model, mostly acting like 3-5 layers of mixing as far as equilibrim dynamics are conscerned over a macroscopic level of only 1-2 uM, but at the sim level this deminsion is enourmous.  Thus I would to the developers propose a wall table set that may help reduce the sizes concerned.  I should aslo add for Astrophysics type things, say the earth atmosphere, at the extreem altitudes, you have layering of gases, Vs. Mixing of these below a specific altitude, or conversly density from pressure and garvity (close to the surfaces of the planet, but mostly applicable to large atoms such as Radon or Ar).  These higher areas are a few 100 meters to few feet, but behave like a liquid liquid interface.  This is increasingly important to fields modeling foreighn atmospheres, examples like Jupiter or a far off planet where you can get the mixture percentages and density, but need to then model these based in size and mass would be say 10K ATM, and an area where gravity or not begin to play a roll.

 

Thaughts suggestions, etc...would be intersting.  Or grants for somone...

 

Sincerely,

 

Stephan Watkins

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[gmx-users] water molecule can not be settled

[Shima Arasteh]

Hi all,

I am trying to simulate a system of protein and lipid bilayer ( in this case 
POPC). The ff I am using is CHARMM36 and I used related settings from 
literature.

I used InflateGRO to pack the lipids around my protein. Then put a position 
restraint on my protein and P atoms of POPC. With these position restraints I 
ran NVT for 1ns and NPT for around10 ns. 
( I need to say that NPT has been done in three steps:  1.First 5ns with 
position restraint on whole protein and P atoms 
2. Then 3 ns with position restraint on just protein atoms 
3. And finally 1 ns with position restraint on protein without H atoms. )
In fact, I tried to prevent any crash by sudden changes.


Next, I tried to run MDRUN, but I get the error of "some water molecules can 
not be settled". This means that my system has not been equiliberated 
sufficiently. OK, what should I do? How can I solve it? Water molecules can not 
be deleted in this step because I will get another fatal error as a result.

My system seems fine. The pressure and energy plots don't show anything 
unusual. But I dont know how can I solve the problem. Would you please give me 
any suggestions?
Reducing the timestep and also changing the thermostat could not help my system 
to overcome this problem. What would be the best solution?

 
Sincerely,
Shima
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[gmx-users] surface tension-crash at step 0

[Elisabeth]

Hi all,

I have problem ruunning NVT with Z direction extended to get surface
tension of a polymer packed in a cell. I tried the same procedure for an
alkane and NVT works well however for the polymer the run crashes at the
very first step..

Doe anyone have clue what wrong could be? Many thanks.

starting mdrun 'Polymer'
1000 steps,  1.0 ps.
step 0
[node6:14338] *** Process received signal ***
[node6:14339] *** Process received signal ***
[node6:14338] Signal: Segmentation fault (11)
[node6:14338] Signal code: Address not mapped (1)
[node6:14338] Failing at address: 0x2fbbaca0
[node6:14339] Signal: Segmentation fault (11)
[node6:14339] Signal code: Address not mapped (1)
[node6:14339] Failing at address: 0x2fbbd2e0
[node6:14339] [ 0] /lib64/libpthread.so.0 [0x3112e0ebe0]
[node6:14339] [ 1] /usr/local/gromacs/lib/libgmx_mpi.so.6 [0x2b2fd8203c54]
[node6:14339] *** End of error message ***
[node6:14338] [ 0] /lib64/libpthread.so.0 [0x3112e0ebe0]
[node6:14338] [ 1] /usr/local/gromacs/lib/libgmx_mpi.so.6 [0x2b4b10e86c65]
[node6:14338] *** End of error message ***
--
mpirun noticed that process rank 3 with PID 14338 on node node6 exited on
signal 11 (Segmentation fault).



On 4 April 2013 12:59, André Farias de Moura  wrote:

> just that simple: as soon as you expand the box in the z direction the
> systems releases the excess pressure by the expansion of the liquid into
> the evacuated region.
>
>
> On Thu, Apr 4, 2013 at 1:20 PM, Elisabeth  wrote:
>
>> Dear Dr. Moura,
>>
>> Thank you for your answer. I equilibrated the cell under NPT and then
>> extended the Z direction to get a surface. Since I run NVT and Z is
>> extended, I see no pressure dependence and surface tension values are
>> similar for all P from 50 to 1000 bar. which is attributed to the fact that
>> Z is extended and system tends to expand regardless of the pressure that
>> was imposed in the initial NPT runs. I have no gas, it is liqiuid-vaccum
>> and wanted to know if there is anyway to capture effect of pressure. From
>> your answer I think there is no such possibility...
>>
>> Please comment if the answer is positive,
>> Thank you
>>
>>
>>
>> On 4 April 2013 10:32, André Farias de Moura  wrote:
>>
>>> There's no simple answer for that. If you apply a lateral pressure (xy
>>> plane) and the system is evacuated in the z direction, the only thing
>>> that
>>> you might expect is that your system would be squeezed in that direction,
>>> and then the lateral pressure would relax.
>>>
>>> If you're thinking about a gas exerting a pressure on the interface, your
>>> system would need to have a pressurized gas instead of vacuum in the z
>>> direction. Please note that pressure would arise from the gas you have
>>> put
>>> into the box and not from an external pressure bath (I would stick to NVT
>>> for such a model). Among the possible issue you might face, the gas would
>>> probably be partially miscible in the liquid phase for high pressures.
>>>
>>> I hope it helps.
>>>
>>> cheers
>>>
>>> Andre
>>>
>>>
>>> On Wed, Apr 3, 2013 at 11:07 PM, Elisabeth  wrote:
>>>
>>> > Hello all,
>>> >
>>> > Does anyone know how one can study the effect of pressure on surface
>>> > tension of pure liquids?
>>> >
>>> > Thanks,
>>> > --
>>> > gmx-users mailing listgmx-users@gromacs.org
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > * Please search the archive at
>>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> > www interface or send it to gmx-users-requ...@gromacs.org.
>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> >
>>> >
>>>
>>>
>>> --
>>> _
>>>
>>> Prof. Dr. André Farias de Moura
>>> Department of Chemistry
>>> Federal University of São Carlos
>>> São Carlos - Brazil
>>> phone: +55-16-3351-8090
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>
>
> --
> _
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
>
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Re: [gmx-users] Intel compiling failed

[Albert]

On 04/05/2013 12:38 PM, Carsten Kutzner wrote:

Hi Albert,

one reason for the error you see could be that you are using a non-Intel
MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.

Carsten



thanks a lot both Carsten and Justin.

I've compiled both fftw and openmpi with intel icc and ifort well. 
However, when I try to compile gromacs, it failed?:



cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda 
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 
-DCMAKE_PREFIX_PATH=/home/albert/install/fftw-3.3.3 
-DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpiCC 
-DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpicc




[  0%] [  0%] [  0%] [  0%] Building NVCC (Device) object 
src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
Building NVCC (Device) object 
src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
Building NVCC (Device) object 
src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
Building NVCC (Device) object 
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o

cc1plus: error: unrecognized command line option '-ip'
cc1plus: error: unrecognized command line option '-ip'
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
  Error generating
/home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


cc1plus: error: unrecognized command line option '-ip'make[2]: *** 
[src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] 
Error 1

cc1plus: error: unrecognized command line option '-ip'
make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs

CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:198 (message):
  Error generating
/home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o


make[2]: *** 
[src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_copyrite_gpu.cu.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message):
  Error generating
/home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o


CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:198 (message):
  Error generating
/home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o


make[2]: *** 
[src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] 
Error 1
make[2]: *** 
[src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] 
Error 1

make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
make: *** [all] Error 2


best
Albert
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[gmx-users] Re: surface tension-crash at step 0

[Dr. Vitaly Chaban]

> Hi all,
>
> I have problem ruunning NVT with Z direction extended to get surface
> tension of a polymer packed in a cell. I tried the same procedure for an
> alkane and NVT works well however for the polymer the run crashes at the
> very first step..
>
> Doe anyone have clue what wrong could be? Many thanks.
>
> starting mdrun 'Polymer'
> 1000 steps,  1.0 ps.
> step 0
> [node6:14338] *** Process received signal ***
>



 Hmmm. Is it not easier to get surface tension from bulk simulation??

On your error, I believe you broke some bond when extending your box in Z
direction. Check energies at step 0 to be completely sure.

Dr. Vitaly Chaban
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Fw: [gmx-users] water molecule can not be settled

[Shima Arasteh]

I' d like to know if it is acceptable to change the molecule coordinates to 
solve this problem? 

Some time back, I deleted such a molecule and then I got a fatal error 
containing that the trj file and other inputs are not inconsistent.

Would you please give me suggestions? I need them urgently. I really appreciate 
your help.

 
Sincerely,
Shima

- Forwarded Message -
From: Shima Arasteh 
To: Discussion list for GROMACS users  
Sent: Friday, April 5, 2013 6:25 PM
Subject: [gmx-users] water molecule can not be settled
 


Hi all,

I am trying to simulate a system of protein and lipid bilayer ( in this case 
POPC). The ff I am using is CHARMM36 and I used related settings from 
literature.

I used InflateGRO to pack the lipids around my protein. Then put a position 
restraint on my protein and P atoms of POPC. With these position restraints I 
ran NVT for 1ns and NPT for around10 ns. 
( I need to say that NPT has been done in three steps:  1.First 5ns with 
position restraint on whole protein and P atoms 
2. Then 3 ns with position restraint on just protein atoms 
3. And finally 1 ns with position restraint on protein without H atoms. )
In fact, I tried to prevent any crash by sudden changes.


Next, I tried to run MDRUN, but I get the error of "some water molecules can 
not be settled". This means that my system has not been equiliberated 
sufficiently. OK, what should I do? How can I solve it? Water molecules can not 
be deleted in this step because I will get another fatal error as a result.

My system seems fine. The pressure and energy plots don't show anything 
unusual. But I dont know how can I solve the problem. Would you please give me 
any suggestions?
Reducing the timestep and also changing the thermostat could not help my system 
to overcome this problem. What would be the best solution?

 
Sincerely,
Shima
--
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Re: [gmx-users] Re: surface tension-crash at step 0

[Elisabeth]

Hi Vitaly,

To get surface tension one needs to extend Z to get a surface. From bulk it
is not possible to create a surface.

My problem is NVT crashes at step 0 and no energies or any other output
file is written...


On 5 April 2013 10:25, Dr. Vitaly Chaban  wrote:

> > Hi all,
> >
> > I have problem ruunning NVT with Z direction extended to get surface
> > tension of a polymer packed in a cell. I tried the same procedure for an
> > alkane and NVT works well however for the polymer the run crashes at the
> > very first step..
> >
> > Doe anyone have clue what wrong could be? Many thanks.
> >
> > starting mdrun 'Polymer'
> > 1000 steps,  1.0 ps.
> > step 0
> > [node6:14338] *** Process received signal ***
> >
>
>
>
>  Hmmm. Is it not easier to get surface tension from bulk simulation??
>
> On your error, I believe you broke some bond when extending your box in Z
> direction. Check energies at step 0 to be completely sure.
>
> Dr. Vitaly Chaban
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Intel compiling failed

[Carsten Kutzner]

On Apr 5, 2013, at 4:21 PM, Albert  wrote:

> On 04/05/2013 12:38 PM, Carsten Kutzner wrote:
>> Hi Albert,
>> 
>> one reason for the error you see could be that you are using a non-Intel
>> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
>> 
>> Carsten
> 
> 
> thanks a lot both Carsten and Justin.
> 
> I've compiled both fftw and openmpi with intel icc and ifort well. However, 
> when I try to compile gromacs, it failed?:
Hm, this is another issue now. What version of the Intel compiler are you using?
With icc 13.0 it works for me, but I remember having problems with older 
versions as well.

Carsten

> 
> 
> cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF 
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda 
> -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 
> -DCMAKE_PREFIX_PATH=/home/albert/install/fftw-3.3.3 
> -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpiCC 
> -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpicc
> 
> 
> 
> [  0%] [  0%] [  0%] [  0%] Building NVCC (Device) object 
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> Building NVCC (Device) object 
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
> Building NVCC (Device) object 
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
> Building NVCC (Device) object 
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
> cc1plus: error: unrecognized command line option '-ip'
> cc1plus: error: unrecognized command line option '-ip'
> CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
>  Error generating
> /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
> 
> 
> cc1plus: error: unrecognized command line option '-ip'make[2]: *** 
> [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o]
>  Error 1
> cc1plus: error: unrecognized command line option '-ip'
> make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> 
> CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:198 (message):
>  Error generating
> /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
> 
> 
> make[2]: *** 
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_copyrite_gpu.cu.o]
>  Error 1
> make[2]: *** Waiting for unfinished jobs
> CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message):
>  Error generating
> /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> 
> 
> CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:198 (message):
>  Error generating
> /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
> 
> 
> make[2]: *** 
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
>  Error 1
> make[2]: *** 
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
>  Error 1
> make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
> make: *** [all] Error 2
> 
> 
> best
> Albert
> -- 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] water molecule can not be settled

[Justin Lemkul]

On Fri, Apr 5, 2013 at 9:55 AM, Shima Arasteh
wrote:

>
>
> Hi all,
>
> I am trying to simulate a system of protein and lipid bilayer ( in this
> case POPC). The ff I am using is CHARMM36 and I used related settings from
> literature.
>
> I used InflateGRO to pack the lipids around my protein. Then put a
> position restraint on my protein and P atoms of POPC. With these position
> restraints I ran NVT for 1ns and NPT for around10 ns.
> ( I need to say that NPT has been done in three steps:  1.First 5ns with
> position restraint on whole protein and P atoms
> 2. Then 3 ns with position restraint on just protein atoms
> 3. And finally 1 ns with position restraint on protein without H atoms. )
> In fact, I tried to prevent any crash by sudden changes.
>
>
>
Seems reasonable.


> Next, I tried to run MDRUN, but I get the error of "some water molecules
> can not be settled". This means that my system has not been equiliberated
> sufficiently. OK, what should I do? How can I solve it? Water molecules can
> not be deleted in this step because I will get another fatal error as a
> result.
>
>
http://www.gromacs.org/Documentation/Terminology/Blowing_Up


> My system seems fine. The pressure and energy plots don't show anything
> unusual. But I dont know how can I solve the problem. Would you please give
> me any suggestions?
> Reducing the timestep and also changing the thermostat could not help my
> system to overcome this problem. What would be the best solution?
>
>
Please post a complete .mdp file.

-Justin

-- 



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


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Re: Fw: [gmx-users] water molecule can not be settled

[Justin Lemkul]

On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh
wrote:

> I' d like to know if it is acceptable to change the molecule coordinates
> to solve this problem?
>
>
It's unlikely that some ad hoc change will magically fix a problem.  Energy
minimization should take care of clashes.


> Some time back, I deleted such a molecule and then I got a fatal error
> containing that the trj file and other inputs are not inconsistent.
>
>
Right, because you've now changed the contents of the system.  It no longer
matches the topology and the trajectory would then be discontinuous.

-Justin

-- 



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


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[gmx-users] gmx 4.6 mpi installation through openmpi?

[라지브간디]

Dear gmx users,


I could able to install gmx4.6.1 without MPI option in my cluster, whereas the 
MPI fails to install and gives the following error ( used command line cmake .. 
-DGMX_MPI=ON  -DGMX_BUILD_OWN_FFTW=ON )


CMake Error at cmake/gmxManageMPI.cmake:161 (message):
  MPI support requested, but no MPI compiler found.  Either set the
  C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or
  set the variables reported missing for MPI_C above.
Call Stack (most recent call first):
  CMakeLists.txt:494 (include)




I have also installed openmpi 1.5 version. which mpirun shows /usr/bin/mpirun. 
It seems openmpi installed in /usr/bin/openmpi/


I dont know how to do link this cmake. 


Please need some suggestion. Thanks.
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Re: Fw: [gmx-users] water molecule can not be settled

[Shima Arasteh]

As I visualized the system, I see a water molecule somewhere between lipid 
chains near the protein entrance. This has been happen during NPT. I' d like to 
delete this molecule but with such a kind of fatal error this would impossible. 
So what's the way?  Is there any tricky way to change coordinate of molecule? 
but I seems also impossible becasue PME problem!
So whats the solution? 


 
Sincerely,
Shima



 From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Friday, April 5, 2013 7:42 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled
 






On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh  
wrote:

I' d like to know if it is acceptable to change the molecule coordinates to 
solve this problem?
>
>

It's unlikely that some ad hoc change will magically fix a problem.  Energy 
minimization should take care of clashes.
 
Some time back, I deleted such a molecule and then I got a fatal error 
containing that the trj file and other inputs are not inconsistent.
>
>

Right, because you've now changed the contents of the system.  It no longer 
matches the topology and the trajectory would then be discontinuous.

-Justin
-- 

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

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Re: Fw: [gmx-users] water molecule can not be settled

[Justin Lemkul]

On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
wrote:

> As I visualized the system, I see a water molecule somewhere between lipid
> chains near the protein entrance. This has been happen during NPT. I' d
> like to delete this molecule but with such a kind of fatal error this would
> impossible. So what's the way?  Is there any tricky way to change
> coordinate of molecule? but I seems also impossible becasue PME problem!
> So whats the solution?
>
>
Delete the molecule, adjust your topology (and index file, if necessary),
and start over with the equilibration.

-Justin

-- 



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


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Re: [gmx-users] Intel compiling failed

[Albert]

On 04/05/2013 04:59 PM, Carsten Kutzner wrote:

Hm, this is another issue now. What version of the Intel compiler are you using?
With icc 13.0 it works for me, but I remember having problems with older 
versions as well.

Carsten


I am using 2011 sp2 version. probably I should try the new one

thank you very much
best
Albert
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Re: [gmx-users] Re: surface tension-crash at step 0

[Dr. Vitaly Chaban]

> My problem is NVT crashes at step 0 and no energies or any other output
> file is written...
>
>
>
What about visualizing your interface?








> On 5 April 2013 10:25, Dr. Vitaly Chaban  wrote:
>
>> > Hi all,
>> >
>> > I have problem ruunning NVT with Z direction extended to get surface
>> > tension of a polymer packed in a cell. I tried the same procedure for an
>> > alkane and NVT works well however for the polymer the run crashes at the
>> > very first step..
>> >
>> > Doe anyone have clue what wrong could be? Many thanks.
>> >
>> > starting mdrun 'Polymer'
>> > 1000 steps,  1.0 ps.
>> > step 0
>> > [node6:14338] *** Process received signal ***
>> >
>>
>>
>>
>>  Hmmm. Is it not easier to get surface tension from bulk simulation??
>>
>> On your error, I believe you broke some bond when extending your box in Z
>> direction. Check energies at step 0 to be completely sure.
>>
>> Dr. Vitaly Chaban
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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Re: Fw: [gmx-users] water molecule can not be settled

[Shima Arasteh]

You mean start over the NPT step?


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled

On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
wrote:

> As I visualized the system, I see a water molecule somewhere between lipid
> chains near the protein entrance. This has been happen during NPT. I' d
> like to delete this molecule but with such a kind of fatal error this would
> impossible. So what's the way?  Is there any tricky way to change
> coordinate of molecule? but I seems also impossible becasue PME problem!
> So whats the solution?
>
>
Delete the molecule, adjust your topology (and index file, if necessary),
and start over with the equilibration.

-Justin

-- 



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


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Re: Fw: [gmx-users] water molecule can not be settled

[Justin Lemkul]

On Fri, Apr 5, 2013 at 11:22 AM, Shima Arasteh
wrote:

> You mean start over the NPT step?
>
>
Yes.

-Justin

-- 



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


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Re: [gmx-users] gmx 4.6 mpi installation through openmpi?

[Szilárd Páll]

Hi,

As the error message states, the reason for the failed configuration is
that CMake can't auto-detect MPI which is needed when you are not providing
the MPI compiler wrapper as compiler.

If you want to build with MPI you can either let CMake auto-detect MPI and
just compile with the C compiler or pass "CC=mpicc" to CMake and use the
MPI compiler "magic" instead of detection.

Unfortunately, the new installation instructions don't explain this detail
which was in fact briefly mentioned in the deprecated CMake instructions:
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/Cmake#MPI_build

Cheers,

--
Szilárd


On Fri, Apr 5, 2013 at 5:12 PM, 라지브간디  wrote:

> Dear gmx users,
>
>
> I could able to install gmx4.6.1 without MPI option in my cluster, whereas
> the MPI fails to install and gives the following error ( used command line
> cmake .. -DGMX_MPI=ON  -DGMX_BUILD_OWN_FFTW=ON )
>
>
> CMake Error at cmake/gmxManageMPI.cmake:161 (message):
>   MPI support requested, but no MPI compiler found.  Either set the
>   C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc),
> or
>   set the variables reported missing for MPI_C above.
> Call Stack (most recent call first):
>   CMakeLists.txt:494 (include)
>
>
>
>
> I have also installed openmpi 1.5 version. which mpirun shows
> /usr/bin/mpirun.
> It seems openmpi installed in /usr/bin/openmpi/
>
>
> I dont know how to do link this cmake.
>
>
> Please need some suggestion. Thanks.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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RE: Fw: [gmx-users] water molecule can not be settled

[Luis Felipe Pineda de Castro]

After having followed for longer time the queries sent by some Indian fellows, 
I wonder if it wouldn't more effective to arrange for a GROMACS tutorial 
offered by Justin in an Indian location. Maybe you, the Indian fellows, can 
arrange for the financing and invite Justin to hold such a Tutorial on the  
basics of MD simulations and their implementation in GROMACS. Considering the 
time Justin is spending responding to your queries, maybe because you are 
devoid of adequate supervision or theoretical background, this would be only 
fair. This posting is maybe a little bit off topic, but somehow related.


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Friday, April 05, 2013 5:22 PM
To: Discussion list for GROMACS users
Subject: Re: Fw: [gmx-users] water molecule can not be settled

You mean start over the NPT step?



Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc:
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled

On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
wrote:

> As I visualized the system, I see a water molecule somewhere between lipid
> chains near the protein entrance. This has been happen during NPT. I' d
> like to delete this molecule but with such a kind of fatal error this would
> impossible. So what's the way?  Is there any tricky way to change
> coordinate of molecule? but I seems also impossible becasue PME problem!
> So whats the solution?
>
>
Delete the molecule, adjust your topology (and index file, if necessary),
and start over with the equilibration.

-Justin

--



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

[Albert]

Hello:

 I am trying to run umbrella sampling, the system contains a ligand. 
here is the pulling setting:


; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= Y N N
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = LIG
pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2



I am trying to run with command:

grompp -f md_pull.mdp -c npt.gro -p complex.top -n index.ndx -o pull.tpr


but it failed with messages:


--
The center of mass of the position restraint coord's is  4.491 3.784  3.540
Pull group 0 'Protein' has 4661 atoms
Pull group 1 'LIG' has 30 atoms
Number of degrees of freedom in T-Coupling group Protein_LIG is 9315.71
Number of degrees of freedom in T-Coupling group Water_and_ions is 85476.30
Largest charge group radii for Van der Waals: 5.945, 5.940 nm
Largest charge group radii for Coulomb:   5.954, 5.951 nm

WARNING 1 [file md_pull.mdp]:
  The sum of the two largest charge group radii (11.905330) is larger than
  rlist (1.20)


Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x64x60, spacing 0.112 0.118 0.118
Pull group  natoms  pbc atom  distance at start reference at t=0
   0  4661  2331
   130  4676   0.682 0.682
Estimate for the relative computational load of the PME mesh part: 0.17
This run will generate roughly 906 Mb of data

There was 1 note

There was 1 warning

---
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1584

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Just Give Me a Blip" (F. Black)

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[gmx-users] RDF output has no data

[Venkat Reddy]

Dear users

I have used AMBER MD package to run simulation for a solvent box. I am now
using the gromacs utility to calculate rdf as follows:

g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg

However, I get no data in the output rdf.xvg. Since Im using specially
generated force field parameters, I do not know how to go about generating
a tpr file (in case that is the problem). The rdf.ndx file is correct for
my atom selection. Please suggest how to go about solving this.

Thank you
-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] genion doesn't work in 4.6.1?

[Albert]

Hello:

 I found that there would be some problem of genion in 4.6.1:

grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr

NOTE 1 [file complex.top, line 44008]:
  System has non-zero total charge: -11.00
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.


genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom

Reading file ions.tpr, VERSION 4.6.1 (single precision)
Using a coulomb cut-off of 1.2 nm
No ions to add and no potential to calculate.

Obviously, the total charge of the system is -11.0, but genion doesn't 
add anything to netural it



thank you very much
best
Albert

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Re: [gmx-users] genion doesn't work in 4.6.1?

[Warren Gallin]

Don't you have to give tyne name of the positive and negative ions that will be 
added by genion?  Otherwise, how would it know?

Warren Gallin

On 2013-04-05, at 1:05 PM, Albert  wrote:

> Hello:
> 
> I found that there would be some problem of genion in 4.6.1:
> 
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
> 
> NOTE 1 [file complex.top, line 44008]:
>  System has non-zero total charge: -11.00
>  Total charge should normally be an integer. See
>  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>  for discussion on how close it should be to an integer.
> 
> 
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom
> 
> Reading file ions.tpr, VERSION 4.6.1 (single precision)
> Using a coulomb cut-off of 1.2 nm
> No ions to add and no potential to calculate.
> 
> Obviously, the total charge of the system is -11.0, but genion doesn't add 
> anything to netural it
> 
> 
> thank you very much
> best
> Albert
> 
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Re: [gmx-users] genion doesn't work in 4.6.1?

[Justin Lemkul]

On Fri, Apr 5, 2013 at 3:05 PM, Albert  wrote:

> Hello:
>
>  I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
>
> NOTE 1 [file complex.top, line 44008]:
>   System has non-zero total charge: -11.00
>   Total charge should normally be an integer. See
>   
> http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetic
>   for discussion on how close it should be to an integer.
>
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom
>
> Reading file ions.tpr, VERSION 4.6.1 (single precision)
> Using a coulomb cut-off of 1.2 nm
> No ions to add and no potential to calculate.
>
> Obviously, the total charge of the system is -11.0, but genion doesn't add
> anything to netural it
>
>
> thank you very much
> best
> Albert
>
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>



-- 



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


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Re: [gmx-users] genion doesn't work in 4.6.1?

[Justin Lemkul]

On Fri, Apr 5, 2013 at 3:05 PM, Albert  wrote:

> Hello:
>
>  I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
>
> NOTE 1 [file complex.top, line 44008]:
>   System has non-zero total charge: -11.00
>   Total charge should normally be an integer. See
>   
> http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetic
>   for discussion on how close it should be to an integer.
>
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom
>
> Reading file ions.tpr, VERSION 4.6.1 (single precision)
> Using a coulomb cut-off of 1.2 nm
> No ions to add and no potential to calculate.
>
> Obviously, the total charge of the system is -11.0, but genion doesn't add
> anything to netural it
>
>
>
genion has never done anything if you just use -neutral. You need to use
-neutral in conjunction with -conc, otherwise manually specify the number
of ions to add.

-Justin

-- 



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


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Re: [gmx-users] problem of umbrella sampling pulling code

[Justin Lemkul]

On Fri, Apr 5, 2013 at 2:03 PM, Albert  wrote:

> Hello:
>
>  I am trying to run umbrella sampling, the system contains a ligand. here
> is the pulling setting:
>
> ; Pull code
> pull= umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim= Y N N
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = Protein
> pull_group1 = LIG
> pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
>
>
> I am trying to run with command:
>
> grompp -f md_pull.mdp -c npt.gro -p complex.top -n index.ndx -o pull.tpr
>
>
> but it failed with messages:
>
>
> --**
> The center of mass of the position restraint coord's is  4.491 3.784  3.540
> Pull group 0 'Protein' has 4661 atoms
> Pull group 1 'LIG' has 30 atoms
> Number of degrees of freedom in T-Coupling group Protein_LIG is 9315.71
> Number of degrees of freedom in T-Coupling group Water_and_ions is 85476.30
> Largest charge group radii for Van der Waals: 5.945, 5.940 nm
> Largest charge group radii for Coulomb:   5.954, 5.951 nm
>
> WARNING 1 [file md_pull.mdp]:
>   The sum of the two largest charge group radii (11.905330) is larger than
>   rlist (1.20)
>
>
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 80x64x60, spacing 0.112 0.118 0.118
> Pull group  natoms  pbc atom  distance at start reference at t=0
>0  4661  2331
>130  4676   0.682 0.682
> Estimate for the relative computational load of the PME mesh part: 0.17
> This run will generate roughly 906 Mb of data
>
> There was 1 note
>
> There was 1 warning
>
> --**-
> Program grompp, VERSION 4.5.5
> Source code file: grompp.c, line: 1584
>
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at 
> http://www.gromacs.org/**Documentation/Errors
> --**-
>
> "Just Give Me a Blip" (F. Black)
>
>
You either have massive charge groups (i.e. a bad topology) or your
molecules are broken across periodic boundaries (which would be the case if
the charge group size was roughly equivalent to the size of one of your box
vectors).

-Justin

-- 



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


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Re: [gmx-users] genion doesn't work in 4.6.1?

[Albert]

On 04/05/2013 09:09 PM, Warren Gallin wrote:

Don't you have to give tyne name of the positive and negative ions that will be 
added by genion?  Otherwise, how would it know?

Warren Gallin


No, it doesn't work either:

genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral 
-norandom -pname NA -nname CL


or

genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral 
-norandom -pname NA -pq 11


Reading file ions.tpr, VERSION 4.6.1 (single precision)
Using a coulomb cut-off of 1.2 nm
No ions to add and no potential to calculate.


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Re: [gmx-users] RDF output has no data

[Justin Lemkul]

On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy  wrote:

> Dear users
>
> I have used AMBER MD package to run simulation for a solvent box. I am now
> using the gromacs utility to calculate rdf as follows:
>
> g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
>
> However, I get no data in the output rdf.xvg. Since Im using specially
> generated force field parameters, I do not know how to go about generating
> a tpr file (in case that is the problem). The rdf.ndx file is correct for
> my atom selection. Please suggest how to go about solving this.
>
>
Blank output usually indicates the command failed, which should have been
preceded by a rather obvious fatal error. If a .tpr file is required, g_rdf
will tell you (again, a fatal error).

-Justin

-- 



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


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Re: [gmx-users] genion doesn't work in 4.6.1?

[Justin Lemkul]

On Fri, Apr 5, 2013 at 3:09 PM, Warren Gallin  wrote:

> Don't you have to give tyne name of the positive and negative ions that
> will be added by genion?  Otherwise, how would it know?
>
>
Default names are used (see genion -h), and the default names are correct
for all force fields as of version 4.5, which standardized ion nomenclature
across force fields.

-Justin

-- 



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


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Re: [gmx-users] genion doesn't work in 4.6.1?

[Abhishek Acharya]

> On 04/05/2013 09:09 PM, Warren Gallin wrote:
>> Don't you have to give tyne name of the positive and negative ions that
>> will be added by genion?  Otherwise, how would it know?
>>
>> Warren Gallin
>
> No, it doesn't work either:
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
> -norandom -pname NA -nname CL
>
> or
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
> -norandom -pname NA -pq 11
>
> Reading file ions.tpr, VERSION 4.6.1 (single precision)
> Using a coulomb cut-off of 1.2 nm
> No ions to add and no potential to calculate.
>
You are using the wrong combinations of flags:
 Either of the following should do the job:
genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11 -pq 1
or
genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral
(incase you want a NaCl conc of 0.15 M. Only in this case, genion will
automatically add NA and CL ions to neutralize the charge and sufficiently
reach the given conc., in this case 0.15 M)

Cheers.
Abhishek Acharya
Structural and Computational Biology Lab
Indian Institute of Technology Kanpur


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RE: [gmx-users] genion doesn't work in 4.6.1?

[Luis Felipe Pineda de Castro]

Again and again posting from Abhishek Acharya or Shima, or Rama David or 
somehow else ... pls read my posting before, it could be useful for you, Indian 
fellows ... maybe it's possible to get some kind of agreement though 
brahmin.net or so ..

Best regards of somebody experienced with Indian "science" 

Best,

Felipe


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Abhishek Acharya [aacha...@iitk.ac.in]
Sent: Friday, April 05, 2013 9:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genion doesn't work in 4.6.1?

> On 04/05/2013 09:09 PM, Warren Gallin wrote:
>> Don't you have to give tyne name of the positive and negative ions that
>> will be added by genion?  Otherwise, how would it know?
>>
>> Warren Gallin
>
> No, it doesn't work either:
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
> -norandom -pname NA -nname CL
>
> or
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
> -norandom -pname NA -pq 11
>
> Reading file ions.tpr, VERSION 4.6.1 (single precision)
> Using a coulomb cut-off of 1.2 nm
> No ions to add and no potential to calculate.
>
You are using the wrong combinations of flags:
 Either of the following should do the job:
genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11 -pq 1
or
genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral
(incase you want a NaCl conc of 0.15 M. Only in this case, genion will
automatically add NA and CL ions to neutralize the charge and sufficiently
reach the given conc., in this case 0.15 M)

Cheers.
Abhishek Acharya
Structural and Computational Biology Lab
Indian Institute of Technology Kanpur


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Re: [gmx-users] Re: surface tension-crash at step 0

[Dr. Vitaly Chaban]

But you have conf.gro


On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth  wrote:

> Well I am not getting the trajectory. Simulation crashes before any step
> is calculated :(
>
>
> On 5 April 2013 11:20, Dr. Vitaly Chaban  wrote:
>
>>
>>
>>> My problem is NVT crashes at step 0 and no energies or any other output
>>> file is written...
>>>
>>>
>>>
>> What about visualizing your interface?
>>
>>
>>
>>
>>
>>
>>
>>
>>> On 5 April 2013 10:25, Dr. Vitaly Chaban  wrote:
>>>
 > Hi all,
 >
 > I have problem ruunning NVT with Z direction extended to get surface
 > tension of a polymer packed in a cell. I tried the same procedure for
 an
 > alkane and NVT works well however for the polymer the run crashes at
 the
 > very first step..
 >
 > Doe anyone have clue what wrong could be? Many thanks.
 >
 > starting mdrun 'Polymer'
 > 1000 steps,  1.0 ps.
 > step 0
 > [node6:14338] *** Process received signal ***
 >



  Hmmm. Is it not easier to get surface tension from bulk simulation??

 On your error, I believe you broke some bond when extending your box in
 Z
 direction. Check energies at step 0 to be completely sure.

 Dr. Vitaly Chaban
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>>>
>>>
>>
>
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RE: [gmx-users] genion doesn't work in 4.6.1?

[Abhishek Acharya]

> Again and again posting from Abhishek Acharya or Shima, or Rama David or
> somehow else ... pls read my posting before, it could be useful for you,
> Indian fellows ... maybe it's possible to get some kind of agreement
> though brahmin.net or so ..
>
> Best regards of somebody experienced with Indian "science"
>
> Best,
>
> Felipe

Dear Luis
I hope you do realize that this is a open for all forum to discuss and
sort out problems. And also that posting such prejudiced comments are not
in the right spirit for this or any other forum related to science. But
since you have posted I would take the opportunity for once to point out
that if there were any shortage of supervision, there would be about a
1000 queries alone from Indians each day. So the take home message is that
only people who don't have anyone in the vicinity to solve their problems
and are stuck, post questions on this forum, and this is not in any way a
function of the geographical region or race a person belongs. Can happen
to anyone.
I hope in the future you don't bring your personal prejudices, whatever
may be your experience with Indian science, into this forum.

With Regards
Abhishek Acharya
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Abhishek Acharya [aacha...@iitk.ac.in]
> Sent: Friday, April 05, 2013 9:35 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] genion doesn't work in 4.6.1?
>
>> On 04/05/2013 09:09 PM, Warren Gallin wrote:
>>> Don't you have to give tyne name of the positive and negative ions that
>>> will be added by genion?  Otherwise, how would it know?
>>>
>>> Warren Gallin
>>
>> No, it doesn't work either:
>>
>> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
>> -norandom -pname NA -nname CL
>>
>> or
>>
>> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
>> -norandom -pname NA -pq 11
>>
>> Reading file ions.tpr, VERSION 4.6.1 (single precision)
>> Using a coulomb cut-off of 1.2 nm
>> No ions to add and no potential to calculate.
>>
> You are using the wrong combinations of flags:
>  Either of the following should do the job:
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11
> -pq 1
> or
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral
> (incase you want a NaCl conc of 0.15 M. Only in this case, genion will
> automatically add NA and CL ions to neutralize the charge and sufficiently
> reach the given conc., in this case 0.15 M)
>
> Cheers.
> Abhishek Acharya
> Structural and Computational Biology Lab
> Indian Institute of Technology Kanpur
>
>
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Re: [gmx-users] Re: surface tension-crash at step 0

[Elisabeth]

The structure is taken from the end of previous simulation which terminates
successfully. The initial structure should not be the problem. What I do
only edit the last line (Z direction) of this structure to create vacuum.

This the output from log file.

Charge group distribution at step 0: 81 188 161 159 158 57 72 84
Grid: 3 x 3 x 6 cells
Initial temperature: 425.057 K

Started mdrun on node 0 Fri Apr  5 17:16:37 2013

   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.40484e+038.26652e+032.54277e+031.31894e+03   -6.08804e+02
LJ (SR)   Coulomb (SR)  PotentialKinetic En.   Total Energy
8.31491e+051.40229e+038.49817e+054.04825e+094.04910e+09
  Conserved En.Temperature Pressure (bar)
4.04910e+091.12122e+087.78980e+08

and here is the output.log from the previous run (bulk simulation)

DD  step 19998999  vol min/aver 0.918  load imb.: force  2.0%

   Step   Time Lambda
   10001.00.0

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.39477e+038.19320e+032.63606e+031.32991e+03   -5.94134e+02
LJ (SR)   Coulomb (SR)  PotentialKinetic En.   Total Energy
   -4.34831e+031.34243e+031.39539e+041.52157e+042.91697e+04
Temperature Pressure (bar)
4.21421e+025.21511e+02

DD  step 1999  vol min/aver 0.866  load imb.: force  1.0%

   Step   Time Lambda
   20002.00.0

Writing checkpoint, step 2000 at Sat Mar  9 22:16:02 2013


   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.29484e+038.23267e+032.54182e+031.31784e+03   -6.08717e+02
LJ (SR)   Coulomb (SR)  PotentialKinetic En.   Total Energy
   -4.35248e+031.37024e+031.37962e+041.55820e+042.93782e+04
Temperature Pressure (bar)
4.31565e+02   -9.33582e+02

<==  ###  ==>
<  A V E R A G E S  >
<==  ###  ==>

Statistics over 2001 steps using 201 frames

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
5.25008e+038.19447e+032.71542e+031.36750e+03   -5.69335e+02
LJ (SR)   Coulomb (SR)  PotentialKinetic En.   Total Energy
   -4.29465e+031.31685e+031.39803e+041.53404e+042.93207e+04
Temperature Pressure (bar)
4.24873e+021.57552e-01







On 5 April 2013 16:34, Dr. Vitaly Chaban  wrote:

> But you have conf.gro
>
>
> On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth  wrote:
>
>> Well I am not getting the trajectory. Simulation crashes before any step
>> is calculated :(
>>
>>
>> On 5 April 2013 11:20, Dr. Vitaly Chaban  wrote:
>>
>>>
>>>
 My problem is NVT crashes at step 0 and no energies or any other output
 file is written...



>>> What about visualizing your interface?
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
 On 5 April 2013 10:25, Dr. Vitaly Chaban  wrote:

> > Hi all,
> >
> > I have problem ruunning NVT with Z direction extended to get surface
> > tension of a polymer packed in a cell. I tried the same procedure
> for an
> > alkane and NVT works well however for the polymer the run crashes at
> the
> > very first step..
> >
> > Doe anyone have clue what wrong could be? Many thanks.
> >
> > starting mdrun 'Polymer'
> > 1000 steps,  1.0 ps.
> > step 0
> > [node6:14338] *** Process received signal ***
> >
>
>
>
>  Hmmm. Is it not easier to get surface tension from bulk simulation??
>
> On your error, I believe you broke some bond when extending your box
> in Z
> direction. Check energies at step 0 to be completely sure.
>
> Dr. Vitaly Chaban
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>>>
>>
>
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[gmx-users] About PP/PME

[陈照云]

I'm running gromacs in parallel.I have 6 nodes.There are 96 cores. But hoiw
to reduce the load imbalance and improve the performance?
The PME-node is 16 and the PP-node is 80.How to divide?
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Re: [gmx-users] About PP/PME

[Justin Lemkul]

On Fri, Apr 5, 2013 at 10:03 PM, 陈照云  wrote:

> I'm running gromacs in parallel.I have 6 nodes.There are 96 cores. But hoiw
> to reduce the load imbalance and improve the performance?
> The PME-node is 16 and the PP-node is 80.How to divide?
>

Generally, if you're losing a lot of performance, mdrun writes this
information near the end of the .log file and tells you how to improve it.
 What you're using is a rather significant imbalance between PP and PME.
 Are you setting -npme manually or letting mdrun decide?  Normally, mdrun
guesses pretty well.  The ratio of PP/PME it decides depends on your .mdp
settings and how much work the PME part is supposed to do.  For triclinic
unit cells, a 3:1 PP/PME ratio is usually best.  For dodecahedral or
octahedral unit cells, 2:1 PP/PME.

-Justin

-- 



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


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[gmx-users] Fwd: Improve performance

[陈照云]

Hi!
I have some questions.
1. Is there any method for me to improve my mdrun performance?
I have read the manual,and tested some option of mdrun,such as
-rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that.
2. Can gromacs 4.6.1 support K20?
   I want to use CPU+GPU. But I met some question when I compiled the mdrun
with k20.The question is that it can't find libopenmm.But I have installed
openmm5.1.I have no idea.

Thanks!
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Re: [gmx-users] Fwd: Improve performance

[Justin Lemkul]

On Fri, Apr 5, 2013 at 10:51 PM, 陈照云  wrote:

> Hi!
> I have some questions.
> 1. Is there any method for me to improve my mdrun performance?
> I have read the manual,and tested some option of mdrun,such as
> -rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that.
>

It is usually unnecessary to mess with these settings. We have absolutely
no way to help you without knowing what system you're simulating, available
hardware, etc.


> 2. Can gromacs 4.6.1 support K20?
>I want to use CPU+GPU. But I met some question when I compiled the mdrun
> with k20.The question is that it can't find libopenmm.But I have installed
> openmm5.1.I have no idea.
>
>
OpenMM may not even build properly any more, and it certainly is not
required to make use of GPU accelerators.  K20 cards should definitely give
you good performance.  As I recall, Erik was using one in the webinar just
a few days ago.

-Justin

-- 



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


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Re: [gmx-users] Topology file-residue unknown

[Juliette N.]

Thank you Justin. I have now the topology. I have a quick question
regarding atom types. I used opls_143 and opls_144 for C and H of ethylene
respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe
these are not the proper atomtypes for H2C=CH2.

rtp entry:

[ atoms ]
   C1opls_143-0.1201
   H11   opls_144 0.0601
   H12   opls_144 0.0601
   C2opls_143-0.1202
   H21   opls_144 0.0602
   H22   opls_144 0.0602

>From atomtypes.atp

opls_141   12.01100  ; alkene C (R2-C=)
 opls_142   12.01100  ; alkene C (RH-C=)
* opls_143   12.01100  ; alkene C (H2-C=)
 opls_1441.00800  ; alkene H (H-C=)*

Did I select the correct atomtypes?
Thanks many times!




On 4 April 2013 18:23, Justin Lemkul  wrote:

>
>
> On 4/4/13 6:17 PM, Juliette N. wrote:
>
>> Hi Justin,
>>
>> Thanks a lot for your message. I am petrified why pdb2gmx is not
>> recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
>> but as you may see below it is not read from rtp.
>>
>> I am sure this residue is added to ffoplsaa.rtp which is existing in the
>> working directory:
>>
>> [ ETY ]
>>   [ atoms ]
>> C1opls_143-0.1201
>> H11   opls_144 0.0601
>> H12   opls_144 0.0601
>> C2opls_143-0.1202
>> H21   opls_144 0.0602
>> H22   opls_144 0.0602
>>
>> [ bonds ]
>> C1H11
>> C1H12
>> C1C2
>> C2H21
>> C2H22
>>;C2C1
>>
>> Then I issue:
>>
>> pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa
>>   :-)  G  R  O  M  A  C  S  (-:
>>
>>GROwing Monsters And Cloning Shrimps
>>
>>  :-)  VERSION 4.5.4  (-:
>>
>> Using the Oplsaa force field in directory oplsaa.ff
>>
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**watermodels.dat
>>
>> Select the Water Model:
>>   1: TIP4P  TIP 4-point, recommended
>>   2: TIP3P  TIP 3-point
>>   3: TIP5P  TIP 5-point
>>   4: SPCsimple point charge
>>   5: SPC/E  extended simple point charge
>>   6: None
>> 6
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.r2b
>> Reading Ethylene.gro...
>> Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms
>> Analyzing pdb file
>> Splitting PDB chains based on TER records or changing chain id.
>> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
>>
>>chain  #res #atoms
>>1 ' ' 1  6
>>
>> No occupancies in Ethylene.gro
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomtypes.atp
>> Atomtype 1
>> Reading residue database... (oplsaa)
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.rtp
>> Residue 56
>> Sorting it all out...
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.hdb
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.n.tdb
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**aminoacids.c.tdb
>>
>> Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1#
>> Processing chain 1 (6 atoms, 1 residues)
>> There are 0 donors and 0 acceptors
>> There are 0 hydrogen bonds
>> Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA.
>> Problem with chain definition, or missing terminal residues.
>> This chain does not appear to contain a recognized chain molecule.
>> If this is incorrect, you can edit residuetypes.dat to modify the
>> behavior.
>> 8 out of 8 lines of specbond.dat converted successfully
>>
>> --**-
>> Program pdb2gmx, VERSION 4.5.4
>> Source code file: resall.c, line: 581
>>
>> Fatal error:
>> Residue 'ETY' not found in residue topology database
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>>
>>
>> I am kind of baffled what could be wrong. I would really appreciate if you
>> could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
>> doubt)?
>> Do i have to edit esiduetypes.dat?
>>
>>
> You've added the .rtp entry incorrectly.  pdb2gmx in version 4.5 and above
> needs .rtp files to be organized in force field subdirectories (in your
> case oplsaa.ff).  It will not recognize a file called "ffoplsaa.rtp," which
> is the pre-4.5 syntax for force field files.
>
>
> -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
>
> ==**==
> --

Re: [gmx-users] RDF output has no data

[Venkat Reddy]

There was no fatal error preceding the output. After selecting the groups
following are the output on the screen
Reading frame   1 time0.100
Warning: can not make broken molecules whole without a run input file,
 don't worry, mdrun doesn't write broken molecules

Reading frame2000 time  200.000


gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman)

And the rdf.xvg file looks like this

#This file was created Sat Apr  6 10:54:13 2013
# by the following command:
# g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
#
# g_rdf is part of G R O M A C S:
#
# GROningen MAchine for Chemical Simulation
#
@title "Radial Distribution"
@xaxis  label "r"
@yaxis  label ""
@TYPE xy
@ subtitle "O21-H2_&_CAT"
 0.001  1
~

Whats going wrong? Please help.


On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul  wrote:

> On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy  wrote:
>
> > Dear users
> >
> > I have used AMBER MD package to run simulation for a solvent box. I am
> now
> > using the gromacs utility to calculate rdf as follows:
> >
> > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
> >
> > However, I get no data in the output rdf.xvg. Since Im using specially
> > generated force field parameters, I do not know how to go about
> generating
> > a tpr file (in case that is the problem). The rdf.ndx file is correct for
> > my atom selection. Please suggest how to go about solving this.
> >
> >
> Blank output usually indicates the command failed, which should have been
> preceded by a rather obvious fatal error. If a .tpr file is required, g_rdf
> will tell you (again, a fatal error).
>
> -Justin
>
> --
>
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] nstxout, nstvout, . . .

[dina dusti]

Dear Specialists 


I am a beginner at Gromacs. I work with MARTINI CG force field.

I selected 5 for 

nstxout        = 5    
nstvout        = 5        
nstenergy    = 5
nstlog        = 5    
nstxtcout    = 5

and my jobs have been finished. 

I found that this time is very large. Is there a way for correct this time? Or, 
should I do these jobs again?!
May I ask you to help me, Please?
Best Regards
Dina

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[gmx-users] amber99 with berger's lipids

[James Starlight]

Dear Gromacs Users!


I'm looking for cut-offs parameters which would be suitable for the
simulation of the membrane proteins (bergers united-atom lipids) with the
amber-99 force fields (full-atomic protein representation). I'd be thankful
to anyone who can provide me with such cut-offs for vdw as well as coulomb
interactions for that force field.



James
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Re: [gmx-users] nstxout, nstvout, . . .

[Chandan Choudhury]

You need to re submit the jobs, with decreased time.


--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Sat, Apr 6, 2013 at 11:20 AM, dina dusti  wrote:

> Dear Specialists
>
>
> I am a beginner at Gromacs. I work with MARTINI CG force field.
>
> I selected 5 for
>
> nstxout= 5
> nstvout= 5
> nstenergy= 5
> nstlog= 5
> nstxtcout= 5
>
> and my jobs have been finished.
>
> I found that this time is very large. Is there a way for correct this
> time? Or, should I do these jobs again?!
> May I ask you to help me, Please?
> Best Regards
> Dina
>
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