Re: [gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

[Mark Abraham]

You don't "turn on" those modifiers, you choose to shift the potential. (In
the future there might be more options.) Shifting the potential is quite
different from the action of vdwtype=shift, see manual 4.1, 7.3. The
potential should be the integral of the force, if you want it to mean
anything. Whether that's important depends what you're doing and want to
observe. The potential is irrelevant if you are just sampling space to see
what is there, but it's critical if you're trying to compute thermodynamic
properties.

Mark


On Thu, May 23, 2013 at 10:46 PM, Bin Liu  wrote:

> Dear Mark,
>
> Could you elaborate on your answer? In my group cutoff scheme, I used
>
> ns_type = grid  ; search neighboring grid cels
> nstlist = 5 ; 10 fs
> rlist   = 1.3   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.3   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
> vdwtype = Shift
> rvdw_switch = 0.9
>
> What is the advantage of turning on coulomb-modifier and vdw-modifier in
> terms of physical or chemical accuracy of simulations? Thanks.
>
> Bin
>
>
>
> Those modifiers shift only the potential, as manual 7.3 points out. So the
> forces and sampling are unaffected, so it does not surprise me that APL is
> unaffected by the use of such a shift. If your group cutoff scheme was
> unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the
> observed difference is significant, then that could be the reason.
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Re: [gmx-users] Re: REMD analysis

[bharat gupta]

Dear Sir,

I tried a lot to understand the meaning and relation between the .log file
and relica_index file, but I was not able to break the code. I tried to
look into gmx forum for some clue, but didn't find any. So, if possible can
you explain it ...

Replica exchange at step 1000 time 2
Repl 0 <-> 1  dE = -1.067e+00
Repl ex  0 x  123456789   10   11   12 x 13
Repl pr   1.0   .01   .68   .21   .05   .09   .26


Replica exchange at step 2000 time 4
Repl ex  01 x  23456789   10   11   12   13
Repl pr.91   .32   .00   .07   .18   .08

output of replica_index.xvg

0   0123456789   10   11   12
13
2   1023456789   10   11   13
12
4   1203456789   10   11   13
12

On Thu, May 23, 2013 at 11:20 PM, Mark Abraham wrote:

> Looked fine
>
>
> On Thu, May 23, 2013 at 4:13 PM, bharat gupta  >wrote:
>
> > Sir,
> >
> > What about the description of replica_temp file that I posted in last
> mail.
> > I think that's correct ... If you can comment on that, I can move on with
> > replica_index file...
> >
> >
> > On Thu, May 23, 2013 at 10:58 PM, Mark Abraham  > >wrote:
> >
> > > It's a demux. One might want trajectories to be at constant
> temperature,
> > or
> > > constant replica. The two files define the (mutually inverse) mappings
> > > between those representations. So one file tells you which replica is
> at
> > > each temperature, and the other which temperature holds each replica.
> > > Nobody's ever written down anything about which is which, so like I
> said
> > a
> > > week back, look at the first few exchanges, see how those are
> represented
> > > in the files, and decide for yourself which file's columns/rows have
> > useful
> > > information you want to look at. And do write that decision down! :-)
> > >
> > > Mark
> > >
> > >
> > > On Thu, May 23, 2013 at 2:55 PM, simula_460  > > >wrote:
> > >
> > > > I checked the md.log and replica_temp.xvg file , what I understood is
> > > that
> > > > the 'x' means swapping and replica are written this way.
> > > > For eg.
> > > > Replica exchange at step 1000 time 2
> > > > Repl 0 <-> 1  dE = -1.067e+00
> > > > Repl ex  0 x  123456789   10   11
> 12
> > x
> > > 13
> > > > Repl pr   1.0   .01   .68   .21   .05   .09
> > .26
> > > >
> > > > output in replica_temp file will be
> > > > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > > >
> > > > It means that replica 1 at higher temp. exchange with the one in
> lower
> > > temp
> > > > 0.
> > > >
> > > > Replica exchange at step 2000 time 4
> > > > Repl ex  01 x  23456789   10   11
> 12
> > > 13
> > > > Repl pr.91   .32   .00   .07   .18   .08
> > > >
> > > > output in replica_temp file will be
> > > > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > > > 2 0 1 3 4 5 6 7 8 9 10 11 13 12
> > > >
> > > > [order is from low to high temp]
> > > >
> > > > But I am not able to understand for replica_index file :-
> > > >
> > > > for the above two time steps here's the output :-
> > > > 0   0123456789   10   11
> > 12
> > > > 13
> > > > 2   1023456789   10   11
> > 13
> > > > 12
> > > > 4   1203456789   10   11
> > 13
> > > > 12
> > > >
> > > > The time step four is different here, I don't know why ?? Ideally the
> > > > output should be same in both files, I suppose ??
> > > >
> > > > Also, I tried to plot for each column separately , here I want to
> > clarify
> > > > that whether each column represents the time evolution of each
> replica
> > > over
> > > > time. For eg. the second column should represent the temp evolution
> for
> > > > replica No. 0 wrt to time. Presuming that I understood it correctly,
> I
> > > > plotted the temp. evolution over time of all replicas separately .
> > Here's
> > > > the replica_temp plot for replicas 0 to 13.
> > > >
> > > > https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > View this message in context:
> > > >
> http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html
> > > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > > --
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> > > >
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> 

[gmx-users] Re: NVT and NPT for small peptide

[maggin]

Thank you very much!



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Re: [gmx-users] tpr of extend simulation

[Mark Abraham]

Use gmxcheck to compare those .tpr files. They should show only the number
of steps differ. So for the purposes of g_hbond knowing the topology, the
two tpr files are equally useful.

Mark


On Fri, May 24, 2013 at 8:25 AM, maggin  wrote:

>  Hi, I run MD production 10ns, and get file: md_0_1.trr, md_0_1.tpr
>
> but simulation time is not enough, so I extend the time to 20ns,
> tpbconv -s md_0_1.tpr  -extend 1  -o md_0_1_next1.tpr
> and get file:  traj.trr, md_0_1_next1.tpr
>
> trajectory cconnection : trjcat -f md_0_1.trr traj.trr -o traj_all_md.trr
>
> So, I have a question when I analysis trajectory use g_hbond
>
> g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg
>
> at here I use md_0_1_next1.tpr,  if is it right ?  I have some not sure
>
> Thank you!
>
>
>
> --
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[gmx-users] g_hbond

[maggin]

# This file was created Fri May 24 13:03:14 2013
# by the following command:
# g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg 
#
# g_hbond is part of G R O M A C S:
#
# Green Red Orange Magenta Azure Cyan Skyblue
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 0  74 517
 2  73 515
 4  69 515
 6  69 529
 8  78 525
10  74 517
12  68 516
14  68 524
16  71 520
   
hi, anybody can tell me at here if Hydrogen bonds Refers to the middle
column: 74,73,69,69,78,74,68,68,71

Thank you !

maggin




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Re: [gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[Mark Abraham]

The GROMACS 4 JCTC paper reports some protocols and comparative results
with NVE working well, IIRC.

Mark


On Thu, May 23, 2013 at 11:59 PM, cyberjhon  wrote:

> Hi Guys
>
> I have been trying by all means to get a real good Energy conservation in
> NVE simulations using gromacs
> but it has been almost impossible for me.
> I have tried many different combinations of Coulomb and VdW parameters and
> changed the cut off radius and nothing.
> 1. Have you ever obtained energy conservation in Gromacs?
> 2. Under what conditions ? for what system?
> 2. Do you have a set of parameters that works to obtain energy
> conservation?
> if you can share with me the mdp file, I will appreciate it.
> My system is Human Papiloma Virus  virus-like particle T=1 inmersed in SPC
> water.
>
> Thanks
>
> John Michael Espinsoa Duran
>
>
>
> --
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[gmx-users] tpr of extend simulation

[maggin]

 Hi, I run MD production 10ns, and get file: md_0_1.trr, md_0_1.tpr

but simulation time is not enough, so I extend the time to 20ns, 
tpbconv -s md_0_1.tpr  -extend 1  -o md_0_1_next1.tpr
and get file:  traj.trr, md_0_1_next1.tpr

trajectory cconnection : trjcat -f md_0_1.trr traj.trr -o traj_all_md.trr

So, I have a question when I analysis trajectory use g_hbond

g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg 

at here I use md_0_1_next1.tpr,  if is it right ?  I have some not sure

Thank you!



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Re: [gmx-users] On using CO2 as solvent

[Justin Lemkul]

On 5/23/13 6:21 PM, Bao Kai wrote:

Hi, all,

Following the tutorial on building biphasic system from Justin, I put the
decane in a box and equilibrated it first.  Then I increased the size of
the box.

Then I wanted to put some CO2 molecules to make a biphasic system.

When I used the following command to do that, I can only add 16 co2
molecules, which is really weird.
genbox_d -cp d10_newbox.gro -cs co2.gro -o d10_solv.gro -p d104.top

Resulting image can be found from the following link.
https://www.dropbox.com/s/slvqfrf4gftu9al/CO2_solvent.png

When I used
  genbox_d -cp d10_newbox.gro -cs  -o d10_solv.gro -p d104.top

More than 4000 water molecules were added.

Could you please tell me what happened here?



The -cs option builds a grid of solvent configurations within the available 
volume of the box contained in -cp.  Presumably co2.gro either contains only one 
molecule in a large box, or it contains molecules that are very far apart.  In 
contrast, spc216.gro is a typical condensed-phase water configuration with lots 
of molecules.



How to use co2 to be the solvent?



The setup depends on exactly what you intend to do.  If decane is a liquid, is 
CO2?  Are you trying to set up a liquid-gas interface?  Are you trying to use 
CO2 as a liquid (presumably at some very cold temperature)?  In any case, you 
need to provide whatever you believe to be a reasonable representation of CO2 as 
your "solvent" to -cs, or add a predefined number of molecules using -ci -nmol.


-Justin

--


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


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[gmx-users] On using CO2 as solvent

[Bao Kai]

Hi, all,

Following the tutorial on building biphasic system from Justin, I put the
decane in a box and equilibrated it first.  Then I increased the size of
the box.

Then I wanted to put some CO2 molecules to make a biphasic system.

When I used the following command to do that, I can only add 16 co2
molecules, which is really weird.
genbox_d -cp d10_newbox.gro -cs co2.gro -o d10_solv.gro -p d104.top

Resulting image can be found from the following link.
https://www.dropbox.com/s/slvqfrf4gftu9al/CO2_solvent.png

When I used
 genbox_d -cp d10_newbox.gro -cs  -o d10_solv.gro -p d104.top

More than 4000 water molecules were added.

Could you please tell me what happened here?

How to use co2 to be the solvent?

Thank you very much.

Best Regards,
Kai
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[gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[cyberjhon]

Hi Guys

I have been trying by all means to get a real good Energy conservation in
NVE simulations using gromacs
but it has been almost impossible for me. 
I have tried many different combinations of Coulomb and VdW parameters and
changed the cut off radius and nothing.
1. Have you ever obtained energy conservation in Gromacs?
2. Under what conditions ? for what system? 
2. Do you have a set of parameters that works to obtain energy conservation?
if you can share with me the mdp file, I will appreciate it.
My system is Human Papiloma Virus  virus-like particle T=1 inmersed in SPC
water.

Thanks

John Michael Espinsoa Duran



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Re: [gmx-users] file not found

[Humayun Arafat]

Thanks for the suggestion.
Currently I do cmake inside  a build directory under Gromacs folder.

cmake .. -DGMX_MPI=OFF   -DGMX_GPU=ON  -DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_INSTALL_PREFIX=/lus/scratch/mmm/gm_82
make
make install

I deleted everything before start.

-- Installing: /lus/scratch/mmm/gm_82/lib/pkgconfig/libgmx.pc
-- Installing: /lus/scratch/mmm/gm_82/lib/libmd.a
-- Installing: /lus/scratch/mmm/gm_82/lib/pkgconfig/libmd.pc
CMake Error at src/kernel/cmake_install.cmake:146 (FILE):
  file INSTALL cannot find
  "/lus/scratch/mmm/gromacs-release-4-6/build/src/kernel/grompp".
Call Stack (most recent call first):
  src/cmake_install.cmake:51 (INCLUDE)
  cmake_install.cmake:51 (INCLUDE)

Please give me some suggestions and let me know if you need all the logs.

thanks
Humayun

On Thu, May 23, 2013 at 3:25 PM, Mark Abraham wrote:

> I've never seen anything like that. Note that the build directories are
> non-relocatable. I'd encourage a) rm -rf * your build directories and
> trying again, and b) testing the performance of code compiled with Cray's
> compiler with that of gcc (which we expect to do much better).
>
> Mark
>
>
> On Thu, May 23, 2013 at 10:06 PM, Humayun Arafat 
> wrote:
>
> > Hi,
> >
> > Gromacs install fails ta the make install command.
> >
> > This is the output.
> > CMake Error at src/kernel/cmake_install.cmake:92 (FILE):
> >   file INSTALL cannot find
> >   "/lus/scratch/mmm/gromacs-release-4-6/build_8.2/src/kernel/grompp".
> > Call Stack (most recent call first):
> >   src/cmake_install.cmake:45 (INCLUDE)
> >   cmake_install.cmake:45 (INCLUDE)
> >
> >
> > I am using Cray compilers.
> > I tried with cmake 2.8.4/8/11
> >
> > Thanks for the help.
> > Humayun
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[gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

[Bin Liu]

Dear Mark,

Could you elaborate on your answer? In my group cutoff scheme, I used

ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.3   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.3   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
vdwtype = Shift
rvdw_switch = 0.9

What is the advantage of turning on coulomb-modifier and vdw-modifier in
terms of physical or chemical accuracy of simulations? Thanks.

Bin



Those modifiers shift only the potential, as manual 7.3 points out. So the
forces and sampling are unaffected, so it does not surprise me that APL is
unaffected by the use of such a shift. If your group cutoff scheme was
unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the
observed difference is significant, then that could be the reason.
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Re: [gmx-users] file not found

[Mark Abraham]

I've never seen anything like that. Note that the build directories are
non-relocatable. I'd encourage a) rm -rf * your build directories and
trying again, and b) testing the performance of code compiled with Cray's
compiler with that of gcc (which we expect to do much better).

Mark


On Thu, May 23, 2013 at 10:06 PM, Humayun Arafat  wrote:

> Hi,
>
> Gromacs install fails ta the make install command.
>
> This is the output.
> CMake Error at src/kernel/cmake_install.cmake:92 (FILE):
>   file INSTALL cannot find
>   "/lus/scratch/mmm/gromacs-release-4-6/build_8.2/src/kernel/grompp".
> Call Stack (most recent call first):
>   src/cmake_install.cmake:45 (INCLUDE)
>   cmake_install.cmake:45 (INCLUDE)
>
>
> I am using Cray compilers.
> I tried with cmake 2.8.4/8/11
>
> Thanks for the help.
> Humayun
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Re: [gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

[Mark Abraham]

If one is using the potential for something (e.g. reweighting, replica
exchange) then now the possibility of a systematic deviation with shifted
potentials is real.

Mark


On Thu, May 23, 2013 at 10:11 PM, Mark Abraham wrote:

> Those modifiers shift only the potential, as manual 7.3 points out. So the
> forces and sampling are unaffected, so it does not surprise me that APL is
> unaffected by the use of such a shift. If your group cutoff scheme was
> unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the
> observed difference is significant, then that could be the reason.
>
> Mark
>
>
>
> On Thu, May 23, 2013 at 9:44 PM, Bin Liu  wrote:
>
>> Hi All,
>>
>> In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable
>> OpenMP parallelization and GPU acceleration. Then some new run parameters
>> are introduced to control the use of Verlet cutoff scheme. However, I
>> noticed the GROMACS manual doesn't give in-depth knowledge on some
>> parameters. For example, I am sure whether and how to use
>> the coulomb-modifier and vdw-modifier parameters with Verlet cutoff
>> scheme.
>> My shallow experience told me these two parameters won't affect the
>> simulation much in term of speed and accuracy. I did a rough benchmark on
>> a
>> DMPC128 bilayer (323K) system to check the area per lipid against
>> (traditional) group cutoff scheme results.
>>
>> Group cutoff scheme: 0.656 (0.008) nm^2   (Uncertainty)
>>
>> Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier =
>> Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet)  0.643nm^2
>>
>> Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None,
>> vdw-modifier = None)  0.645nm^2
>>
>> Basically the results from two Verlet cutoff parameter sets are
>> indistinguishable. I am looking forward to your help to give me some
>> insight into this question.
>>
>> Thank you very much.
>>
>> Regards
>>
>> Bin
>> --
>> 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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>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

[Mark Abraham]

Those modifiers shift only the potential, as manual 7.3 points out. So the
forces and sampling are unaffected, so it does not surprise me that APL is
unaffected by the use of such a shift. If your group cutoff scheme was
unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the
observed difference is significant, then that could be the reason.

Mark


On Thu, May 23, 2013 at 9:44 PM, Bin Liu  wrote:

> Hi All,
>
> In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable
> OpenMP parallelization and GPU acceleration. Then some new run parameters
> are introduced to control the use of Verlet cutoff scheme. However, I
> noticed the GROMACS manual doesn't give in-depth knowledge on some
> parameters. For example, I am sure whether and how to use
> the coulomb-modifier and vdw-modifier parameters with Verlet cutoff scheme.
> My shallow experience told me these two parameters won't affect the
> simulation much in term of speed and accuracy. I did a rough benchmark on a
> DMPC128 bilayer (323K) system to check the area per lipid against
> (traditional) group cutoff scheme results.
>
> Group cutoff scheme: 0.656 (0.008) nm^2   (Uncertainty)
>
> Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier =
> Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet)  0.643nm^2
>
> Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None,
> vdw-modifier = None)  0.645nm^2
>
> Basically the results from two Verlet cutoff parameter sets are
> indistinguishable. I am looking forward to your help to give me some
> insight into this question.
>
> Thank you very much.
>
> Regards
>
> Bin
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] file not found

[Humayun Arafat]

Hi,

Gromacs install fails ta the make install command.

This is the output.
CMake Error at src/kernel/cmake_install.cmake:92 (FILE):
  file INSTALL cannot find
  "/lus/scratch/mmm/gromacs-release-4-6/build_8.2/src/kernel/grompp".
Call Stack (most recent call first):
  src/cmake_install.cmake:45 (INCLUDE)
  cmake_install.cmake:45 (INCLUDE)


I am using Cray compilers.
I tried with cmake 2.8.4/8/11

Thanks for the help.
Humayun
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[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

[Bin Liu]

Hi All,

In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable
OpenMP parallelization and GPU acceleration. Then some new run parameters
are introduced to control the use of Verlet cutoff scheme. However, I
noticed the GROMACS manual doesn't give in-depth knowledge on some
parameters. For example, I am sure whether and how to use
the coulomb-modifier and vdw-modifier parameters with Verlet cutoff scheme.
My shallow experience told me these two parameters won't affect the
simulation much in term of speed and accuracy. I did a rough benchmark on a
DMPC128 bilayer (323K) system to check the area per lipid against
(traditional) group cutoff scheme results.

Group cutoff scheme: 0.656 (0.008) nm^2   (Uncertainty)

Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier =
Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet)  0.643nm^2

Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None,
vdw-modifier = None)  0.645nm^2

Basically the results from two Verlet cutoff parameter sets are
indistinguishable. I am looking forward to your help to give me some
insight into this question.

Thank you very much.

Regards

Bin
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Re: [gmx-users] mdrun generate a lot of files with #

[Mark Abraham]

Or take your backup life into your own hands and set the environment
variable GMX_MAXBACKUP=-1

Mark


On Thu, May 23, 2013 at 7:04 PM, Justin Lemkul  wrote:

>
>
> On 5/23/13 12:53 PM, mu xiaojia wrote:
>
>> Dear users,
>>
>> I have used gromacs a while, however, sometime, when I run it on
>> supercomputer-clusters, I saw mdrun will generate a lot of files with "#",
>> which occupied a lot of space, does anyone know why and how to avoid it?
>>
>> Thanks
>>
>> example, my command"mdrun_mpi -s -deffnm job -cpi -append"
>>
>> then besides ordinary md result files,  it will also generate things like:
>>
>> #job.xtc.1#   #job.xvg.1#  job
>>
>>
> These are backups of previous runs that have been issued with the same
> command.  All Gromacs commands have this behavior - rather than overwriting
> your files, it backs them up.  Either clean up your directories prior to
> issuing your commands, or use unique file names or directories.
>
> -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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> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> * Can't post? Read 
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>
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Re: [gmx-users] mdrun generate a lot of files with #

[Justin Lemkul]

On 5/23/13 12:53 PM, mu xiaojia wrote:

Dear users,

I have used gromacs a while, however, sometime, when I run it on
supercomputer-clusters, I saw mdrun will generate a lot of files with "#",
which occupied a lot of space, does anyone know why and how to avoid it?

Thanks

example, my command"mdrun_mpi -s -deffnm job -cpi -append"

then besides ordinary md result files,  it will also generate things like:

#job.xtc.1#   #job.xvg.1#  job



These are backups of previous runs that have been issued with the same command. 
 All Gromacs commands have this behavior - rather than overwriting your files, 
it backs them up.  Either clean up your directories prior to issuing your 
commands, or use unique file names or directories.


-Justin

--


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


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[gmx-users] mdrun generate a lot of files with #

[mu xiaojia]

Dear users,

I have used gromacs a while, however, sometime, when I run it on
supercomputer-clusters, I saw mdrun will generate a lot of files with "#",
which occupied a lot of space, does anyone know why and how to avoid it?

Thanks

example, my command"mdrun_mpi -s -deffnm job -cpi -append"

then besides ordinary md result files,  it will also generate things like:

#job.xtc.1#   #job.xvg.1#  job
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Re: [gmx-users] Why the shape of the molecules changed?

[Justin Lemkul]

On 5/23/13 11:27 AM, Bao Kai wrote:

Hi,

Thank you for your prompt reply.

I just think since we have added so many constraints on the shape of
the molecules, the molecules should keep their shapes.

I am wrong?  I have not done simulation with such big molecules
before.  I just did some simulations with water and CO2. The case can
be different, right?



Your topology does not indicate any sort of shape constraints, nor should you be 
using any.


-Justin


Thanks,
Kai

On 5/23/13 11:16 AM, Bao Kai wrote:

Hi, all,

I finally wrote a decane topology file. I used it to some simple simulation.

The energy minimization works, while after a simple nvt equilibration,
the shape of the molecules changed.

Please find the images before and after the nvt equilibration from the
following links.
https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png
https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png



I see nothing wrong.  The outcome seems totally normal for an MD
simulation.  If
molecules didn't change their configuration, what would be the point of
simulating? ;)

-Justin




The following is the topology part for the decane molecule.   Please
help to check if there is anything wrong.   C2 and C3 are CH2 and CH3
respectively.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1  3  yes 0.50.5

[ atomtypes ]
;   type  at.nummasschargeptypesigmaepsilon
C2   6 14.02700.0  A0.3740.4301
C3   6 15.035  0.0  A0.3740.6243
[ moleculetype ]
; Namenrexcl
D10 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
   1C3  1D10 1C3  1   0.0 15.035
   ; qtot -0.18
   2C2  1D10 1C2  2  0.0  14.027
; qtot -0.3
   3C2  1D10 2C2  3  0.0  14.027
; qtot -0.42
   4C2  1D10 3C2  4  0.0  14.027
; qtot -0.54
   5C2  1D10 4C2  5  0.0  14.027
; qtot -0.66
   6C2  1D10 5C2  6  0.0  14.027
; qtot -0.78
   7C2  1D10 6C2  7  0.0  14.027
; qtot -0.9
   8C2  1D10 7C2  8  0.0  14.027
; qtot -1.02
   9C2  1D10 8C2  9  0.0  14.027
; qtot -1.14
  10C3  1D10 2C3  10 0.0  15.035
; qtot -1.32


[ bonds ]
;  aiaj functc0c1c2c3
  1 2 1  1.53e-01  543  1.53e-01  543
  2 3 1  1.53e-01  543  1.53e-01  543
  3 4 1  1.53e-01  543  1.53e-01  543
  4 5 1  1.53e-01  543  1.53e-01  543
  5 6 1  1.53e-01  543  1.53e-01  543
  6 7 1  1.53e-01  543  1.53e-01  543
  7 8 1  1.53e-01  543  1.53e-01  543
  8 9 1  1.53e-01  543  1.53e-01  543
  910 1  1.53e-01  543  1.53e-01  543

[ pairs ]
;  aiaj functc0c1c2c3
  1 4 1
  2 5 1
  3 6 1
  4 7 1
  5 8 1
  6 9 1
  710 1

[ angles ]
;  aiajak functc0c1c2c3
  1 2 3 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  2 3 4 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  3 4 5 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  4 5 6 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  5 6 7 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  6 7 8 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  7 8 9 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02
  8 910 2  1.11e+02  4.00e+02  1.11e+02  
4.00e+02

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
  1 2 3 4 3  0.00e+00 5.00e+00  3.00e+00
   0.00e+00 5.00e+00  3.00e+00
  2 3 4 5 3  0.00e+00 5.00e+00  3.00e+00
   0.00e+00 5.00e+00  3.00e+00
  3 4 5 6 3  0.00e+00 5.00e+00  3.00e+00
   0.00e+00 5.00e+00  3.00e+00
  4 5 6 7 3  0.00e+00 5.00e+00  3.00e+00
   0.00e+00 5.00e+00  3.00e+00
  5 6 7 8 3  0.00e+00 5.00e+00  3.00e+00
   0.00e+00 5.00e+0

[gmx-users] Why the shape of the molecules changed?

[Bao Kai]

Hi,

Thank you for your prompt reply.

I just think since we have added so many constraints on the shape of
the molecules, the molecules should keep their shapes.

I am wrong?  I have not done simulation with such big molecules
before.  I just did some simulations with water and CO2. The case can
be different, right?

Thanks,
Kai

On 5/23/13 11:16 AM, Bao Kai wrote:
> Hi, all,
>
> I finally wrote a decane topology file. I used it to some simple simulation.
>
> The energy minimization works, while after a simple nvt equilibration,
> the shape of the molecules changed.
>
> Please find the images before and after the nvt equilibration from the
> following links.
> https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png
> https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png
>

I see nothing wrong.  The outcome seems totally normal for an MD
simulation.  If
molecules didn't change their configuration, what would be the point of
simulating? ;)

-Justin

>
>
> The following is the topology part for the decane molecule.   Please
> help to check if there is anything wrong.   C2 and C3 are CH2 and CH3
> respectively.
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
>  1  3  yes 0.50.5
>
> [ atomtypes ]
> ;   type  at.nummasschargeptypesigmaepsilon
>C2   6 14.02700.0  A0.3740.4301
>C3   6 15.035  0.0  A0.3740.6243
> [ moleculetype ]
> ; Namenrexcl
> D10 3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB  massB
>   1C3  1D10 1C3  1   0.0 15.035
>   ; qtot -0.18
>   2C2  1D10 1C2  2  0.0  14.027
>; qtot -0.3
>   3C2  1D10 2C2  3  0.0  14.027
>; qtot -0.42
>   4C2  1D10 3C2  4  0.0  14.027
>; qtot -0.54
>   5C2  1D10 4C2  5  0.0  14.027
>; qtot -0.66
>   6C2  1D10 5C2  6  0.0  14.027
>; qtot -0.78
>   7C2  1D10 6C2  7  0.0  14.027
>; qtot -0.9
>   8C2  1D10 7C2  8  0.0  14.027
>; qtot -1.02
>   9C2  1D10 8C2  9  0.0  14.027
>; qtot -1.14
>  10C3  1D10 2C3  10 0.0  15.035
>; qtot -1.32
>
>
> [ bonds ]
> ;  aiaj functc0c1c2c3
>  1 2 1  1.53e-01  543  1.53e-01  543
>  2 3 1  1.53e-01  543  1.53e-01  543
>  3 4 1  1.53e-01  543  1.53e-01  543
>  4 5 1  1.53e-01  543  1.53e-01  543
>  5 6 1  1.53e-01  543  1.53e-01  543
>  6 7 1  1.53e-01  543  1.53e-01  543
>  7 8 1  1.53e-01  543  1.53e-01  543
>  8 9 1  1.53e-01  543  1.53e-01  543
>  910 1  1.53e-01  543  1.53e-01  543
>
> [ pairs ]
> ;  aiaj functc0c1c2c3
>  1 4 1
>  2 5 1
>  3 6 1
>  4 7 1
>  5 8 1
>  6 9 1
>  710 1
>
> [ angles ]
> ;  aiajak functc0c1c2
> c3
>  1 2 3 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  2 3 4 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  3 4 5 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  4 5 6 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  5 6 7 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  6 7 8 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  7 8 9 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>  8 910 2  1.11e+02  4.00e+02  1.11e+02  
> 4.00e+02
>
> [ dihedrals ]
> ;  aiajakal functc0c1
> c2c3c4c5
>  1 2 3 4 3  0.00e+00 5.00e+00  3.00e+00
>   0.00e+00 5.00e+00  3.00e+00
>  2 3 4 5 3  0.00e+00 5.00e+00  3.00e+00
>   0.00e+00 5.00e+00  3.00e+00
>  3 4 5 6 3  0.00e+00 5.00e+00  3.00e+00
>   0.00e+00 5.00e+00  3.00e+00
>  4 5 6 7 3  0.00e+00 5.00e+00  3.00e+00
>   0.00e+00 5.00e+00  3.00e+00
>  5 6 7 8 3  0.00e+00 5.00e+00  3.00e+00
>   0.00e+00 5.00e+0

Re: [gmx-users] Why the shape of the molecules changed?

[Justin Lemkul]

On 5/23/13 11:16 AM, Bao Kai wrote:

Hi, all,

I finally wrote a decane topology file. I used it to some simple simulation.

The energy minimization works, while after a simple nvt equilibration,
the shape of the molecules changed.

Please find the images before and after the nvt equilibration from the
following links.
https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png
https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png



I see nothing wrong.  The outcome seems totally normal for an MD simulation.  If 
molecules didn't change their configuration, what would be the point of 
simulating? ;)


-Justin




The following is the topology part for the decane molecule.   Please
help to check if there is anything wrong.   C2 and C3 are CH2 and CH3
respectively.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1  3  yes 0.50.5

[ atomtypes ]
;   type  at.nummasschargeptypesigmaepsilon
   C2   6 14.02700.0  A0.3740.4301
   C3   6 15.035  0.0  A0.3740.6243
[ moleculetype ]
; Namenrexcl
D10 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
  1C3  1D10 1C3  1   0.0 15.035
  ; qtot -0.18
  2C2  1D10 1C2  2  0.0  14.027
   ; qtot -0.3
  3C2  1D10 2C2  3  0.0  14.027
   ; qtot -0.42
  4C2  1D10 3C2  4  0.0  14.027
   ; qtot -0.54
  5C2  1D10 4C2  5  0.0  14.027
   ; qtot -0.66
  6C2  1D10 5C2  6  0.0  14.027
   ; qtot -0.78
  7C2  1D10 6C2  7  0.0  14.027
   ; qtot -0.9
  8C2  1D10 7C2  8  0.0  14.027
   ; qtot -1.02
  9C2  1D10 8C2  9  0.0  14.027
   ; qtot -1.14
 10C3  1D10 2C3  10 0.0  15.035
   ; qtot -1.32


[ bonds ]
;  aiaj functc0c1c2c3
 1 2 1  1.53e-01  543  1.53e-01  543
 2 3 1  1.53e-01  543  1.53e-01  543
 3 4 1  1.53e-01  543  1.53e-01  543
 4 5 1  1.53e-01  543  1.53e-01  543
 5 6 1  1.53e-01  543  1.53e-01  543
 6 7 1  1.53e-01  543  1.53e-01  543
 7 8 1  1.53e-01  543  1.53e-01  543
 8 9 1  1.53e-01  543  1.53e-01  543
 910 1  1.53e-01  543  1.53e-01  543

[ pairs ]
;  aiaj functc0c1c2c3
 1 4 1
 2 5 1
 3 6 1
 4 7 1
 5 8 1
 6 9 1
 710 1

[ angles ]
;  aiajak functc0c1c2c3
 1 2 3 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 2 3 4 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 3 4 5 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 4 5 6 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 5 6 7 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 6 7 8 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 7 8 9 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
 8 910 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
 1 2 3 4 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 2 3 4 5 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 3 4 5 6 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 4 5 6 7 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 5 6 7 8 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 6 7 8 9 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 7 8 910 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00


[system]
sparkling water
[molecules]
D10 208

Thank you very much.

Best Regards,
Kai



--


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

[gmx-users] Why the shape of the molecules changed?

[Bao Kai]

Hi, all,

I finally wrote a decane topology file. I used it to some simple simulation.

The energy minimization works, while after a simple nvt equilibration,
the shape of the molecules changed.

Please find the images before and after the nvt equilibration from the
following links.
https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png
https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png



The following is the topology part for the decane molecule.   Please
help to check if there is anything wrong.   C2 and C3 are CH2 and CH3
respectively.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1  3  yes 0.50.5

[ atomtypes ]
;   type  at.nummasschargeptypesigmaepsilon
  C2   6 14.02700.0  A0.3740.4301
  C3   6 15.035  0.0  A0.3740.6243
[ moleculetype ]
; Namenrexcl
D10 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
 1C3  1D10 1C3  1   0.0 15.035
 ; qtot -0.18
 2C2  1D10 1C2  2  0.0  14.027
  ; qtot -0.3
 3C2  1D10 2C2  3  0.0  14.027
  ; qtot -0.42
 4C2  1D10 3C2  4  0.0  14.027
  ; qtot -0.54
 5C2  1D10 4C2  5  0.0  14.027
  ; qtot -0.66
 6C2  1D10 5C2  6  0.0  14.027
  ; qtot -0.78
 7C2  1D10 6C2  7  0.0  14.027
  ; qtot -0.9
 8C2  1D10 7C2  8  0.0  14.027
  ; qtot -1.02
 9C2  1D10 8C2  9  0.0  14.027
  ; qtot -1.14
10C3  1D10 2C3  10 0.0  15.035
  ; qtot -1.32


[ bonds ]
;  aiaj functc0c1c2c3
1 2 1  1.53e-01  543  1.53e-01  543
2 3 1  1.53e-01  543  1.53e-01  543
3 4 1  1.53e-01  543  1.53e-01  543
4 5 1  1.53e-01  543  1.53e-01  543
5 6 1  1.53e-01  543  1.53e-01  543
6 7 1  1.53e-01  543  1.53e-01  543
7 8 1  1.53e-01  543  1.53e-01  543
8 9 1  1.53e-01  543  1.53e-01  543
910 1  1.53e-01  543  1.53e-01  543

[ pairs ]
;  aiaj functc0c1c2c3
1 4 1
2 5 1
3 6 1
4 7 1
5 8 1
6 9 1
710 1

[ angles ]
;  aiajak functc0c1c2c3
1 2 3 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
2 3 4 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
3 4 5 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
4 5 6 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
5 6 7 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
6 7 8 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
7 8 9 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02
8 910 2  1.11e+02  4.00e+02  1.11e+02  4.00e+02

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
1 2 3 4 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00
2 3 4 5 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00
3 4 5 6 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00
4 5 6 7 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00
5 6 7 8 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00
6 7 8 9 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00
7 8 910 3  0.00e+00 5.00e+00  3.00e+00
 0.00e+00 5.00e+00  3.00e+00


[system]
sparkling water
[molecules]
D10 208

Thank you very much.

Best Regards,
Kai
-- 
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Re: [gmx-users] Re: How to restrain dihedral angles to reserve the tacticity?

[Javier Cerezo]

Improper dihedrals (section 4.2.11) can be used to retain chirality 
within unitied atoms models.


Javier


El 23/05/13 13:48, Abhishek Acharya escribió:

Dear Acharya,
Thank you very much for this quick reply. According to your suggestion, I
measure the main chain dihedral angles, only to find that same values are
obtained for both isotactic and syndiotactic ones.

That is obvious i think for a correct tacticity polymeric chain.

Therefore, this way can
not distinguish tacticity of polymer chains.

I don't understand what is the need as the atomic positions should be the
enough to distinguish tacticity.

For a good initial
configuration (with a correct tacticity), due to higher energy barrier,
the
tacticity of polymer can be naturally reserved using the improper
dihedrals
or restrained dihedrals as you suggest during the MD simulation. However,
for a bad initial configuration (with an incorrect tacticity), your way
seems not to be able yield the desirable results. Could you provide
further
help, please? Thanks a lot.

The suggestion was assuming a good initial configuration. However, i do
not have sufficient expertise to further comment on this.

Cheers
Abhishek




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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Re: [gmx-users] Re: REMD analysis

[Mark Abraham]

Looked fine


On Thu, May 23, 2013 at 4:13 PM, bharat gupta wrote:

> Sir,
>
> What about the description of replica_temp file that I posted in last mail.
> I think that's correct ... If you can comment on that, I can move on with
> replica_index file...
>
>
> On Thu, May 23, 2013 at 10:58 PM, Mark Abraham  >wrote:
>
> > It's a demux. One might want trajectories to be at constant temperature,
> or
> > constant replica. The two files define the (mutually inverse) mappings
> > between those representations. So one file tells you which replica is at
> > each temperature, and the other which temperature holds each replica.
> > Nobody's ever written down anything about which is which, so like I said
> a
> > week back, look at the first few exchanges, see how those are represented
> > in the files, and decide for yourself which file's columns/rows have
> useful
> > information you want to look at. And do write that decision down! :-)
> >
> > Mark
> >
> >
> > On Thu, May 23, 2013 at 2:55 PM, simula_460  > >wrote:
> >
> > > I checked the md.log and replica_temp.xvg file , what I understood is
> > that
> > > the 'x' means swapping and replica are written this way.
> > > For eg.
> > > Replica exchange at step 1000 time 2
> > > Repl 0 <-> 1  dE = -1.067e+00
> > > Repl ex  0 x  123456789   10   11   12
> x
> > 13
> > > Repl pr   1.0   .01   .68   .21   .05   .09
> .26
> > >
> > > output in replica_temp file will be
> > > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > >
> > > It means that replica 1 at higher temp. exchange with the one in lower
> > temp
> > > 0.
> > >
> > > Replica exchange at step 2000 time 4
> > > Repl ex  01 x  23456789   10   11   12
> > 13
> > > Repl pr.91   .32   .00   .07   .18   .08
> > >
> > > output in replica_temp file will be
> > > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > > 2 0 1 3 4 5 6 7 8 9 10 11 13 12
> > >
> > > [order is from low to high temp]
> > >
> > > But I am not able to understand for replica_index file :-
> > >
> > > for the above two time steps here's the output :-
> > > 0   0123456789   10   11
> 12
> > > 13
> > > 2   1023456789   10   11
> 13
> > > 12
> > > 4   1203456789   10   11
> 13
> > > 12
> > >
> > > The time step four is different here, I don't know why ?? Ideally the
> > > output should be same in both files, I suppose ??
> > >
> > > Also, I tried to plot for each column separately , here I want to
> clarify
> > > that whether each column represents the time evolution of each replica
> > over
> > > time. For eg. the second column should represent the temp evolution for
> > > replica No. 0 wrt to time. Presuming that I understood it correctly, I
> > > plotted the temp. evolution over time of all replicas separately .
> Here's
> > > the replica_temp plot for replicas 0 to 13.
> > >
> > > https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png
> > >
> > >
> > >
> > >
> > > --
> > > View this message in context:
> > > http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html
> > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > --
> > > 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
> > >
> > --
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: REMD analysis

[bharat gupta]

Sir,

What about the description of replica_temp file that I posted in last mail.
I think that's correct ... If you can comment on that, I can move on with
replica_index file...


On Thu, May 23, 2013 at 10:58 PM, Mark Abraham wrote:

> It's a demux. One might want trajectories to be at constant temperature, or
> constant replica. The two files define the (mutually inverse) mappings
> between those representations. So one file tells you which replica is at
> each temperature, and the other which temperature holds each replica.
> Nobody's ever written down anything about which is which, so like I said a
> week back, look at the first few exchanges, see how those are represented
> in the files, and decide for yourself which file's columns/rows have useful
> information you want to look at. And do write that decision down! :-)
>
> Mark
>
>
> On Thu, May 23, 2013 at 2:55 PM, simula_460  >wrote:
>
> > I checked the md.log and replica_temp.xvg file , what I understood is
> that
> > the 'x' means swapping and replica are written this way.
> > For eg.
> > Replica exchange at step 1000 time 2
> > Repl 0 <-> 1  dE = -1.067e+00
> > Repl ex  0 x  123456789   10   11   12 x
> 13
> > Repl pr   1.0   .01   .68   .21   .05   .09   .26
> >
> > output in replica_temp file will be
> > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> >
> > It means that replica 1 at higher temp. exchange with the one in lower
> temp
> > 0.
> >
> > Replica exchange at step 2000 time 4
> > Repl ex  01 x  23456789   10   11   12
> 13
> > Repl pr.91   .32   .00   .07   .18   .08
> >
> > output in replica_temp file will be
> > 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> > 2 0 1 3 4 5 6 7 8 9 10 11 13 12
> >
> > [order is from low to high temp]
> >
> > But I am not able to understand for replica_index file :-
> >
> > for the above two time steps here's the output :-
> > 0   0123456789   10   11   12
> > 13
> > 2   1023456789   10   11   13
> > 12
> > 4   1203456789   10   11   13
> > 12
> >
> > The time step four is different here, I don't know why ?? Ideally the
> > output should be same in both files, I suppose ??
> >
> > Also, I tried to plot for each column separately , here I want to clarify
> > that whether each column represents the time evolution of each replica
> over
> > time. For eg. the second column should represent the temp evolution for
> > replica No. 0 wrt to time. Presuming that I understood it correctly, I
> > plotted the temp. evolution over time of all replicas separately . Here's
> > the replica_temp plot for replicas 0 to 13.
> >
> > https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png
> >
> >
> >
> >
> > --
> > View this message in context:
> > http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > 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
> >
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Re: [gmx-users] Re: REMD analysis

[Mark Abraham]

It's a demux. One might want trajectories to be at constant temperature, or
constant replica. The two files define the (mutually inverse) mappings
between those representations. So one file tells you which replica is at
each temperature, and the other which temperature holds each replica.
Nobody's ever written down anything about which is which, so like I said a
week back, look at the first few exchanges, see how those are represented
in the files, and decide for yourself which file's columns/rows have useful
information you want to look at. And do write that decision down! :-)

Mark


On Thu, May 23, 2013 at 2:55 PM, simula_460 wrote:

> I checked the md.log and replica_temp.xvg file , what I understood is that
> the 'x' means swapping and replica are written this way.
> For eg.
> Replica exchange at step 1000 time 2
> Repl 0 <-> 1  dE = -1.067e+00
> Repl ex  0 x  123456789   10   11   12 x 13
> Repl pr   1.0   .01   .68   .21   .05   .09   .26
>
> output in replica_temp file will be
> 1 0 2 3 4 5 6 7 8 9 10 11 13 12
>
> It means that replica 1 at higher temp. exchange with the one in lower temp
> 0.
>
> Replica exchange at step 2000 time 4
> Repl ex  01 x  23456789   10   11   12   13
> Repl pr.91   .32   .00   .07   .18   .08
>
> output in replica_temp file will be
> 1 0 2 3 4 5 6 7 8 9 10 11 13 12
> 2 0 1 3 4 5 6 7 8 9 10 11 13 12
>
> [order is from low to high temp]
>
> But I am not able to understand for replica_index file :-
>
> for the above two time steps here's the output :-
> 0   0123456789   10   11   12
> 13
> 2   1023456789   10   11   13
> 12
> 4   1203456789   10   11   13
> 12
>
> The time step four is different here, I don't know why ?? Ideally the
> output should be same in both files, I suppose ??
>
> Also, I tried to plot for each column separately , here I want to clarify
> that whether each column represents the time evolution of each replica over
> time. For eg. the second column should represent the temp evolution for
> replica No. 0 wrt to time. Presuming that I understood it correctly, I
> plotted the temp. evolution over time of all replicas separately . Here's
> the replica_temp plot for replicas 0 to 13.
>
> https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] the details about g_density

[Justin Lemkul]

On 5/23/13 9:32 AM, vigaryang wrote:

Thanks very much for your reply.Fortunately,I have used g_density in NVT systems.  Does 
the expression " it is built from the coordinate origin outward" mean that the 
mass density profile is calculated based on the average of the coordination and weight of 
each atom of the molecule?



You asked if density profiles were built from the center of mass, which they are 
not.  Masses/charges are binned across the desired box vector like histograms, 
with the number of slices (and thus implicitly the bin width determined by the 
-sl option), and bins are constructed from the zero point of the axis upward.


-Justin



With best wishes,

Qiwei Yang


- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Date: 2013-05-23, 19:54:11
Subject: Re: [gmx-users] the details about g_density


On 5/22/13 9:12 PM, vigaryang wrote:

I have used the program "g_density" to generate the mass density profile and 
the charge density profile of molecules at gas-liquid interface. My question is: Is the 
center of mass/charge used by g_density to compute the the mass/charge density profile?



No, it is built from the coordinate origin outward. Note that there are
problems with g_density when using NPT and/or complex systems:

http://redmine.gromacs.org/issues/1168

The issue also has some useful information about how g_density works, which of
course can also be obtained from the code itself.

-Justin


I'm eager for the answer, because the reviewer of my submitted article ask me 
for that question but I don't know how to reply. I have used google to search 
for the answer, but I did not found.

I really appreciate you for the attention and consideration to this email.


Best regards,

Vigar Yang

Department of Chemical and Biological Engineering,
Zhejiang University,
Hangzhou, China










--


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: Re: [gmx-users] the details about g_density

[vigaryang]

Thanks very much for your reply.Fortunately,I have used g_density in NVT 
systems.  Does the expression " it is built from the coordinate origin outward" 
mean that the mass density profile is calculated based on the average of the 
coordination and weight of each atom of the molecule? 


With best wishes,

Qiwei Yang


- Original Message - 
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Date: 2013-05-23, 19:54:11
Subject: Re: [gmx-users] the details about g_density


On 5/22/13 9:12 PM, vigaryang wrote:
> I have used the program "g_density" to generate the mass density profile and 
> the charge density profile of molecules at gas-liquid interface. My question 
> is: Is the center of mass/charge used by g_density to compute the the 
> mass/charge density profile?
>

No, it is built from the coordinate origin outward. Note that there are 
problems with g_density when using NPT and/or complex systems:

http://redmine.gromacs.org/issues/1168

The issue also has some useful information about how g_density works, which of 
course can also be obtained from the code itself.

-Justin

> I'm eager for the answer, because the reviewer of my submitted article ask me 
> for that question but I don't know how to reply. I have used google to search 
> for the answer, but I did not found.
>
> I really appreciate you for the attention and consideration to this email.
>
>
> Best regards,
>
> Vigar Yang
>
> Department of Chemical and Biological Engineering,
> Zhejiang University,
> Hangzhou, China
>
>
>
>

-- 


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


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[gmx-users] Re: REMD analysis

[simula_460]

I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written this way.
For eg.
Replica exchange at step 1000 time 2
Repl 0 <-> 1  dE = -1.067e+00
Repl ex  0 x  123456789   10   11   12 x 13
Repl pr   1.0   .01   .68   .21   .05   .09   .26

output in replica_temp file will be
1 0 2 3 4 5 6 7 8 9 10 11 13 12

It means that replica 1 at higher temp. exchange with the one in lower temp
0.

Replica exchange at step 2000 time 4
Repl ex  01 x  23456789   10   11   12   13
Repl pr.91   .32   .00   .07   .18   .08

output in replica_temp file will be
1 0 2 3 4 5 6 7 8 9 10 11 13 12
2 0 1 3 4 5 6 7 8 9 10 11 13 12

[order is from low to high temp]

But I am not able to understand for replica_index file :-

for the above two time steps here's the output :-
0   0123456789   10   11   12 13
2   1023456789   10   11   13 12
4   1203456789   10   11   13 12

The time step four is different here, I don't know why ?? Ideally the
output should be same in both files, I suppose ??

Also, I tried to plot for each column separately , here I want to clarify
that whether each column represents the time evolution of each replica over
time. For eg. the second column should represent the temp evolution for
replica No. 0 wrt to time. Presuming that I understood it correctly, I
plotted the temp. evolution over time of all replicas separately . Here's
the replica_temp plot for replicas 0 to 13.

https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png




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[gmx-users] Re: REMD analysis

[simula_460]

Dear Sir,

I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written this way.
For eg.
Replica exchange at step 1000 time 2
Repl 0 <-> 1  dE = -1.067e+00
Repl ex  0 x  123456789   10   11   12 x 13
Repl pr   1.0   .01   .68   .21   .05   .09   .26

output in replica_temp file will be
1 0 2 3 4 5 6 7 8 9 10 11 13 12

It means that replica 1 at higher temp. exchange with the one in lower temp
0.

Replica exchange at step 2000 time 4
Repl ex  01 x  23456789   10   11   12   13
Repl pr.91   .32   .00   .07   .18   .08

output in replica_temp file will be
1 0 2 3 4 5 6 7 8 9 10 11 13 12
2 0 1 3 4 5 6 7 8 9 10 11 13 12

[order is from low to high temp]

But I am not able to understand for replica_index file :-

for the above two time steps here's the output :-
0   0123456789   10   11   12 13
2   1023456789   10   11   13 12
4   1203456789   10   11   13 12

The time step four is different here, I don't know why ?? Ideally the
output should be same in both files, I suppose ??

Also, I tried to plot for each column separately , here I want to clarify
that whether each column represents the time evolution of each replica over
time. For eg. the second column should represent the temp evolution for
replica No. 0 wrt to time. Presuming that I understood it correctly, I
plotted the temp. evolution over time of all replicas separately . Here's
the replica_temp plot for replicas 0 to 13.

https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png






--
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Re: [gmx-users] Re: REMD analysis

[bharat gupta]

Dear Sir,

I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written that way.
For eg.
Replica exchange at step 1000 time 2
Repl 0 <-> 1  dE = -1.067e+00
Repl ex  0 x  123456789   10   11   12 x 13
Repl pr   1.0   .01   .68   .21   .05   .09   .26

output in replica_temp file will be
1 0 2 3 4 5 6 7 8 9 10 11 13 12

It means that replica 1 at higher temp. exchange with the one in lower temp
0.

Replica exchange at step 2000 time 4
Repl ex  01 x  23456789   10   11   12   13
Repl pr.91   .32   .00   .07   .18   .08

output in replica_temp file will be
1 0 2 3 4 5 6 7 8 9 10 11 13 12
2 0 1 3 4 5 6 7 8 9 10 11 13 12

[order is from low to high temp]

But I am not able to understand for replica_index file :-

for the above two time steps here's the output :-
0   0123456789   10   11   12
13
2   1023456789   10   11   13
12
4   1203456789   10   11   13
12

The time step four is different here, I don't know why ?? Ideally the
output should be same in both files, I suppose ??

Also, I tried to plot for each column separately , here I want to clarify
that whether each column represents the time evolution of each replica over
time. For eg. the second column should represent the temp evolution for
replica No. 0 wrt to time. Presuming that I understood it correctly, I
plotted the temp. evolution over time of all replicas separately . Here's
the replica_temp plot for replicas 0 to 13.

https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png







On Thu, May 23, 2013 at 5:21 PM, Mark Abraham wrote:

> Each md.log has all the information about all replica exchanges, as you can
> see. I suggested you look at your .log and .xvg files a week ago ;-)
> There's no problem if a script post-processes all the identical information
> from each .log file.
>
> Mark
>
>
> On Thu, May 23, 2013 at 9:01 AM, bharat gupta  >wrote:
>
> > I checked the first 5 md.log files, and the data is exactly the same in
> all
> > of them  Does it mean there could be problem with demux.pl
> >
> >
> > On Thu, May 23, 2013 at 3:53 PM, Mark Abraham  > >wrote:
> >
> > > Look at those files. Use diff. They're all the same. Your plots are
> > > probably all showing the first column of each. You want to look at each
> > > column. (And even then the best it can show is that your simulation is
> > not
> > > clearly inadequate.)
> > >
> > > Mark
> > >
> > >
> > > On Thu, May 23, 2013 at 8:48 AM, bharat gupta <
> bharat.85.m...@gmail.com
> > > >wrote:
> > >
> > > > Dear Sir,
> > > >
> > > > Thank you for your reply. But I used the command demux.pl md$.log ,
> > > where
> > > > $= No. of replica. I get the same plot every time. Sorry to ask this
> ,
> > > but
> > > > where am I going wrong ??
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] the details about g_density

[Justin Lemkul]

On 5/22/13 9:12 PM, vigaryang wrote:

I have used the program "g_density" to generate the mass density profile and 
the charge density profile of molecules at gas-liquid interface. My question is: Is the 
center of mass/charge used by g_density to compute the the mass/charge density profile?



No, it is built from the coordinate origin outward.  Note that there are 
problems with g_density when using NPT and/or complex systems:


http://redmine.gromacs.org/issues/1168

The issue also has some useful information about how g_density works, which of 
course can also be obtained from the code itself.


-Justin


I'm eager for the answer, because the reviewer of my submitted article ask me 
for that question but I don't know how to reply. I have used google to search 
for the answer, but I did not found.

I really appreciate you for the attention and consideration to this email.


Best regards,

Vigar Yang

Department of Chemical and Biological Engineering,
Zhejiang University,
Hangzhou, China






--


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] residue labeling in g_rmsf

[Justin Lemkul]

On 5/23/13 6:51 AM, Arunima Shilpi wrote:

Respected Sir

If i want my residue  name to be labeled in the graph for g_rmsf ,how
should I proceed...

I used the following command

g_rmsf -f md_0_1.xtc -s md_0_1.tpr -res -o  rmsf.xvg



Add labels in your favorite plotting software.  g_rmsf will not write residue 
names.

-Justin

--


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


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Re: [gmx-users] Re: How to restrain dihedral angles to reserve the tacticity?

[Abhishek Acharya]

> Dear Acharya,
> Thank you very much for this quick reply. According to your suggestion, I
> measure the main chain dihedral angles, only to find that same values are
> obtained for both isotactic and syndiotactic ones.
That is obvious i think for a correct tacticity polymeric chain.
> Therefore, this way can
> not distinguish tacticity of polymer chains.
I don't understand what is the need as the atomic positions should be the
enough to distinguish tacticity.
> For a good initial
> configuration (with a correct tacticity), due to higher energy barrier,
> the
> tacticity of polymer can be naturally reserved using the improper
> dihedrals
> or restrained dihedrals as you suggest during the MD simulation. However,
> for a bad initial configuration (with an incorrect tacticity), your way
> seems not to be able yield the desirable results. Could you provide
> further
> help, please? Thanks a lot.
The suggestion was assuming a good initial configuration. However, i do
not have sufficient expertise to further comment on this.

Cheers
Abhishek


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[gmx-users] residue labeling in g_rmsf

[Arunima Shilpi]

Respected Sir

If i want my residue  name to be labeled in the graph for g_rmsf ,how
should I proceed...

I used the following command

g_rmsf -f md_0_1.xtc -s md_0_1.tpr -res -o  rmsf.xvg
-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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[gmx-users] Re: How to restrain dihedral angles to reserve the tacticity?

[xiaowu759]

Dear Acharya,
Thank you very much for this quick reply. According to your suggestion, I
measure the main chain dihedral angles, only to find that same values are
obtained for both isotactic and syndiotactic ones. Therefore, this way can
not distinguish tacticity of polymer chains. For a good initial
configuration (with a correct tacticity), due to higher energy barrier, the
tacticity of polymer can be naturally reserved using the improper dihedrals
or restrained dihedrals as you suggest during the MD simulation. However,
for a bad initial configuration (with an incorrect tacticity), your way
seems not to be able yield the desirable results. Could you provide further
help, please? Thanks a lot.
Yours sincerely,
Chaofu Wu



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Re: [gmx-users] How to restrain dihedral angles to reserve the tacticity?

[Abhishek Acharya]

Hello
I think constraining rotation about all the main chain bonds should be
sufficient to preserve the tacticity. So taking your example, the dihedral
angles could be R1 C1 C2 C1 and C1 C2 C1 R2. Of course  you will have
restrain all similar dihedral angles along the whole length of your
polymer. That should do it.

Cheers
Abhishek

> Dear gmxers,
> I try to reserve the tacticity of polymer chains during the MD
> simulations.
> By searching this mail-list, I find that to restrain dihedral angles
> provides a way to realize it. However, what dihedral angles should I
> restrain? For example, a polymer has a monomer with a chiral carbon C1 and
> a non-chiral carbon C2 on the main chain, and two different side groups
> (i.e. R1 and R2) are attached to C1. Could you give me some hints, please?
> Thanks a lot for any reply to this letter.
> Yours sincerely,
> Chaofu Wu


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Re: [gmx-users] Re: REMD analysis

[Mark Abraham]

Each md.log has all the information about all replica exchanges, as you can
see. I suggested you look at your .log and .xvg files a week ago ;-)
There's no problem if a script post-processes all the identical information
from each .log file.

Mark


On Thu, May 23, 2013 at 9:01 AM, bharat gupta wrote:

> I checked the first 5 md.log files, and the data is exactly the same in all
> of them  Does it mean there could be problem with demux.pl
>
>
> On Thu, May 23, 2013 at 3:53 PM, Mark Abraham  >wrote:
>
> > Look at those files. Use diff. They're all the same. Your plots are
> > probably all showing the first column of each. You want to look at each
> > column. (And even then the best it can show is that your simulation is
> not
> > clearly inadequate.)
> >
> > Mark
> >
> >
> > On Thu, May 23, 2013 at 8:48 AM, bharat gupta  > >wrote:
> >
> > > Dear Sir,
> > >
> > > Thank you for your reply. But I used the command demux.pl md$.log ,
> > where
> > > $= No. of replica. I get the same plot every time. Sorry to ask this ,
> > but
> > > where am I going wrong ??
> > > --
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[gmx-users] If your mails are rejected from the list

[Rossen Apostolov]

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[gmx-users] How to restrain dihedral angles to reserve the tacticity?

[Wu Chaofu]

Dear gmxers,
I try to reserve the tacticity of polymer chains during the MD simulations.
By searching this mail-list, I find that to restrain dihedral angles
provides a way to realize it. However, what dihedral angles should I
restrain? For example, a polymer has a monomer with a chiral carbon C1 and
a non-chiral carbon C2 on the main chain, and two different side groups
(i.e. R1 and R2) are attached to C1. Could you give me some hints, please?
Thanks a lot for any reply to this letter.
Yours sincerely,
Chaofu Wu
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Re: [gmx-users] Re: REMD analysis

[bharat gupta]

I checked the first 5 md.log files, and the data is exactly the same in all
of them  Does it mean there could be problem with demux.pl


On Thu, May 23, 2013 at 3:53 PM, Mark Abraham wrote:

> Look at those files. Use diff. They're all the same. Your plots are
> probably all showing the first column of each. You want to look at each
> column. (And even then the best it can show is that your simulation is not
> clearly inadequate.)
>
> Mark
>
>
> On Thu, May 23, 2013 at 8:48 AM, bharat gupta  >wrote:
>
> > Dear Sir,
> >
> > Thank you for your reply. But I used the command demux.pl md$.log ,
> where
> > $= No. of replica. I get the same plot every time. Sorry to ask this ,
> but
> > where am I going wrong ??
> > --
> > 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
> >
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