Re: [gmx-users] continuation, gmx-users Digest, Vol 102, Issue 99

[Justin Lemkul]

On 10/16/12 1:14 PM, Ali Alizadeh wrote:

Dear Justin

In your opinion, Why did not i get a symmetric results of number density?



The .mdp file does not give any really useful information for this problem, 
except to show that you're using NPT, which I suspect might contribute to the 
problem.  Without plots and hard numbers, it's all hand-waving at this point.


-Justin


this is my md.mdp file:

title   = OPLS
define  =   ;
; Run parameters
integrator  = md;
nsteps  = 100   ;
dt  = 0.001 ;
emtol   = 10.0
emstep  = 0.1
; Output control
nstxout = 10;
nstvout = 10;
nstenergy   = 10;
nstlog  = 10;
nstxtcout   = 10
xtc_precision   = 10
; Bond parameters
continuation= no;
constraint_algorithm = lincs;
constraints = all-bonds ;
lincs_iter  = 1 ;
lincs_order = 4 ;
; Neighborsearching
ns_type = grid  ;
nstlist = 1 ;
rlist   = 1.0   ;
rcoulomb= 1.0   ;
rvdw= 1.0   ;
; Electrostatics
coulombtype = PME   ;
pme_order   = 4 ;
fourierspacing  = 0.16  ;
ewald_geometry  = 3d
; Temperature coupling is on
tcoupl  = berendsen ;
tc-grps = System;
tau_t   = 0.1   ;
ref_t   = 240   ;
; Pressure coupling is on
pcoupl  = berendsen ;
pcoupltype  = isotropic ;
tau_p   = 2.0   ;
ref_p   = 300.0 ;
compressibility = 4.5e-5;
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ;
; Velocity generation
gen_vel = no;





--


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: gmx-users Digest, Vol 102, Issue 99

[Justin Lemkul]

On 10/16/12 11:10 AM, Ali Alizadeh wrote:

Dear Justin

Thank you for your reply,


On 10/16/12 7:55 AM, Ali Alizadeh wrote:

Dear All users

1- When i use these commands for generating number density profile

I see completely different results(in z direction, length in z
direction is 8, number density versus of z)

g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z -symm -center

It's trend is increasing(from z=0 to z=2 then decreasing(fall to zero,
z= 2-5) and then increasing(z=5-7.5)

g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z

But in the case,It's trend is decreasing(z=0-2.5) then
increasing(suddenly to maximum, z=2.5-5) and then decreasing(z=5-8)


 Justin wrote:
You're telling g_density to do two different things.  You
got two different
 results.  I don't see that as odd.

1- I don't know different between them , can you further explain?



If you don't understand the command line options, perhaps you should do a bit 
more background reading and testing to understand them.  In one command, you are 
symmetrizing and centering the system, in another you are not.  Different 
commands will lead to different output.  Images of the plots would be more 
useful than vague descriptions.



2- Number density profile Should be symmetric?


   Justin wrote:
  Only if the system is symmetric.

2- My system is symmetric but unfortunately my number density results
is not symmetric.

3- Can you help me for using correct command for results of number density?



In theory, your first command will produce the desired output.  I can offer no 
explanation as to why your symmetrical system does not appear to be symmetrical. 
 Are you using NPT?  Changes in the box dimensions can mess up box slices in 
g_density.



4- I have three types of molecules, There is one layer of water
between two same layers.

   pbc for all of directions!



Seems like it should be symmetrical, assuming of course that there are an equal 
number of molecules on both sides of the central layer.


-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] losing data in trjconv?

[Lucio Ricardo Montero Valenzuela]

Hello,
you have to use the -force parameter in trjconv, to copy also the forces
in the original trr file.
Best regards
Lucio

El lun, 15-10-2012 a las 21:18 +0800, Gil Claudio escribió:
> Hi Justin,
> 
> My original intention was to lessen the 5 ns trajectory to transfer to 
> another drive. I did
> 
> trjconv -f traj.trr -o traj_1.trr -b 0 -e 4000
> 
> When I saw the resulting file greatly lessened in size, that's when I tried 
> as a test
> 
> trjconv -f traj.trr -o traj_1.trr
> 
> I knew that it was not supposed to do anything, hence my surprise upon seeing 
> the file size decrease by ~25%.
> 
> No other flags were used.
> 
> I'll do your suggestion in 2 days. Am out of the lab till then.
> 
> Thanks
> 
> Gil Claudio
> 
> On Oct 15, 2012, at 7:55 PM, Justin Lemkul  wrote:
> 
> > 
> > 
> > On 10/15/12 7:50 AM, Gil Claudio wrote:
> >> Hi Peter,
> >> 
> >> Same machine, all single precision.
> >> 
> > 
> > Run gmxcheck -f -f2 on the two trajectories to see what's going on.  Can 
> > you explain what you were trying to do?  I see no point in the trjconv 
> > command you ran.  Were there other flags that you haven't shown?  Other 
> > commands that produced strange results that led you to simplify the trjconv 
> > command down to something that (in theory) doesn't do anything?
> > 
> > -Justin
> > 
> >> On Oct 15, 2012, at 5:39 PM, "Peter C. Lai"  wrote:
> >> 
> >>> Was traj.trr output by the same machine/mdrun as the machine you are 
> >>> running
> >>> trjconv on?
> >>> 
> >>> Is traj.trr (or the mdrun that wrote it) double precision and trjconv is
> >>> compiled float (single precision)?
> >>> 
> >>> On 2012-10-15 02:31:00AM -0700, Gil Claudio wrote:
>  Hi all,
>  
>  When I do the following command
>  
>  trjconv -f traj.trr -o traj_1.trr
>  
>  the file size of traj_1.trr is around 25% smaller than traj.trr.
>  
>  Does traj_1.trr contain less data than traj.trr?
>  
>  Thanks
>  
>  Gil
>  --
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> >>> 
> >>> --
> >>> ==
> >>> Peter C. Lai| University of Alabama-Birmingham
> >>> Programmer/Analyst| KAUL 752A
> >>> Genetics, Div. of Research| 705 South 20th Street
> >>> p...@uab.edu| Birmingham AL 35294-4461
> >>> (205) 690-0808|
> >>> ==
> >>> 
> > 
> > -- 
> > 
> > 
> > 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] Fwd:

[Sheyore Omovie]

http://www.ferbras.cl/page..yahoo.php?y=3c4j7ufywe&amjdawe=zaweh
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[gmx-users] Re: gmx-users Digest, Vol 102, Issue 99

[Ali Alizadeh]

Dear Justin

Thank you for your reply,


On 10/16/12 7:55 AM, Ali Alizadeh wrote:
> Dear All users
>
> 1- When i use these commands for generating number density profile
>
> I see completely different results(in z direction, length in z
> direction is 8, number density versus of z)
>
> g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z -symm -center
>
> It's trend is increasing(from z=0 to z=2 then decreasing(fall to zero,
> z= 2-5) and then increasing(z=5-7.5)
>
> g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z
>
> But in the case,It's trend is decreasing(z=0-2.5) then
> increasing(suddenly to maximum, z=2.5-5) and then decreasing(z=5-8)
>
Justin wrote:
   You're telling g_density to do two different things.  You
got two different
results.  I don't see that as odd.

1- I don't know different between them , can you further explain?

> 2- Number density profile Should be symmetric?
>
  Justin wrote:
 Only if the system is symmetric.

2- My system is symmetric but unfortunately my number density results
is not symmetric.

3- Can you help me for using correct command for results of number density?

4- I have three types of molecules, There is one layer of water
between two same layers.

  pbc for all of directions!
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Re: [gmx-users] Re: The problem of converting CGenff parameters to those of Gromacs

[Peter C. Lai]

Just to let you know, charge information in ffnonbonded.itp is ignored. 
pdb2gmx reads charges from the corresponding .rtp file when writing the .gro
file.

On 2012-10-16 06:47:57AM -0700, spin wrote:
> Hi, Peter and David,
> 
> Thank you for your help! I have solve it by David's script.
> 
> Qing Liu
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042p5002079.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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-- 
==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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[gmx-users] Re: Creat a new residue.

[spin]

Hi, Justin,
 
Thank you very much!  Its has been running.

Qing Liu



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Re: [gmx-users] why g_tune_pme generate .trr file?

[Justin Lemkul]

On 10/16/12 10:50 AM, Albert wrote:

hello:

  I am using g_tune_pme to optimize my MD performance by command:

g_tune_pme -np 144 -v -s npt1.tpr -c npt1.gro -launch -x npt1.xtc -g npt1.log


here is the parameters which I used in .mdp file:

; Parameters controlling output writing
; nstxout= 1; Write coordinates to output .trr file every 2 
ps
; nstvout= 1; Write velocities to output .trr file every 2 
ps

nstxtcout=1 ;
nstenergy= 5000; Write energies to output .edr file every 2 ps
nstlog= 5000; Write output to .log file every 2 ps


as we can see, I've removed the output for .trr file, but the g_tune_pme still
generate a .trr file called : traj.trr


I am wondering why it still generate .trr file? is it possible to disable it
generate .trr file? I only need the .xtc file.



If you comment out these lines, the default value (100) is used, which creates 
very big trajectories.  To suppress .trr output, you need to explicitly set 
nstxout, nstvout, and nstfout to zero.


-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] why g_tune_pme generate .trr file?

[Albert]

hello:

 I am using g_tune_pme to optimize my MD performance by command:

g_tune_pme -np 144 -v -s npt1.tpr -c npt1.gro -launch -x npt1.xtc -g 
npt1.log



here is the parameters which I used in .mdp file:

; Parameters controlling output writing
; nstxout= 1; Write coordinates to output .trr file 
every 2 ps
; nstvout= 1; Write velocities to output .trr file 
every 2 ps


nstxtcout=1 ;
nstenergy= 5000; Write energies to output .edr file every 2 ps
nstlog= 5000; Write output to .log file every 2 ps


as we can see, I've removed the output for .trr file, but the g_tune_pme 
still generate a .trr file called : traj.trr



I am wondering why it still generate .trr file? is it possible to 
disable it generate .trr file? I only need the .xtc file.


thank you very much
best
Albert
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Re: [gmx-users] Creat a new residue.

[Justin Lemkul]

On 10/16/12 10:10 AM, spin wrote:

Hello, everyone,

I have created a new residue "CYM" in charmm27 force field. It consists of
the residue "CYS2" and MTSL which bonds to CYS2 by disulfide. The topology
of MTSL have been generated by CGenFF. I have added corresponding data to
aminoacid.rtp, ffbond.itp, ffnonbond.itp, atomtype.atp residuetypes,dat and
the protein's PDB file.  In the aminoacid.rtp, I have add all atoms'
topology information.

Then I type the command:
  /pdb2gmx -f XX.pdb -o XX.gro -p XXtop -ss -his /

but it told me some atoms' missing:

/WARNING: atom HB2 is missing in residue CYM 90 in the pdb file
  You might need to add atom HB2 to the hydrogen database of building
block CYM
  in the file aminoacids.hdb (see the manual)


WARNING: atom O1 is missing in residue CYM 90 in the pdb file


WARNING: atom HN is missing in residue CYM 117 in the pdb file
  You might need to add atom HN to the hydrogen database of building
block CYM
  in the file aminoacids.hdb (see the manual)


WARNING: atom HA is missing in residue CYM 117 in the pdb file
  You might need to add atom HA to the hydrogen database of building
block CYM/
/ in the file aminoacids.hdb (see the manual)


WARNING: atom HB1 is missing in residue CYM 117 in the pdb file
  You might need to add atom HB1 to the hydrogen database of building
block CYM
  in the file aminoacids.hdb (see the manual)


WARNING: atom HB2 is missing in residue CYM 117 in the pdb file
  You might need to add atom HB2 to the hydrogen database of building
block CYM
  in the file aminoacids.hdb (see the manual)


WARNING: atom O1 is missing in residue CYM 117 in the pdb file


---
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1463

Fatal error:
There were 10 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors/

I checked the .hdb file, but it seemed not to require hydrogen adding for
CYS. Moreover, the atoms of MTSL like "O1" are not protein atoms, and they
are described by CGenFF. Now some of them are missing . Can you give me the
solution? Thank you!



Every residue needs its own .hdb entry if your coordinate file does not contain 
all the hydrogens.  Atoms named "O1" and "O2" get confused with terminal oxygen 
atoms.  Use different names and make sure you're not confusing types with 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] Tesla M2075 error...

[Anthony Cruz Balberdi]

Thanks!

On Tue, Oct 16, 2012 at 10:00 AM, Justin Lemkul  wrote:

>
>
> On 10/16/12 9:58 AM, Anthony Cruz Balberdi wrote:
>
>> Hi user:
>>
>> I was able to compile gromacs with GPU support without errors, but when I
>> test it with the benchmark got the following error:
>>
>> (mdrun-gpu -device
>> "OpenMM:platform=Cuda,memtest=**15,deviceid=0,force-device=no" -s
>> topol.tpr
>> -v)
>>
>> Fatal error:
>> The selected GPU (#0, Tesla M2075) is not supported by Gromacs! Most
>> probably you have a low-end GPU which would not perform well, or new
>> hardware that has not been tested with the current release. If you still
>> want to try using the device, use the force-device=yes option.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>>
>> This is normal behaviour or I made something wrong in the configuration?
>> because is clear in the website that Tesla M2075 is supported by gromacs.
>> The only solution is changing force-device to yes?
>>
>>
> Correct.  The list of supported GPU's is outdated in the code and should
> be fixed for the next release.
>
> -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] Creat a new residue.

[spin]

Hello, everyone,

I have created a new residue "CYM" in charmm27 force field. It consists of
the residue "CYS2" and MTSL which bonds to CYS2 by disulfide. The topology
of MTSL have been generated by CGenFF. I have added corresponding data to
aminoacid.rtp, ffbond.itp, ffnonbond.itp, atomtype.atp residuetypes,dat and
the protein's PDB file.  In the aminoacid.rtp, I have add all atoms'
topology information. 

Then I type the command:
 /pdb2gmx -f XX.pdb -o XX.gro -p XXtop -ss -his /

but it told me some atoms' missing:

/WARNING: atom HB2 is missing in residue CYM 90 in the pdb file
 You might need to add atom HB2 to the hydrogen database of building
block CYM
 in the file aminoacids.hdb (see the manual)


WARNING: atom O1 is missing in residue CYM 90 in the pdb file


WARNING: atom HN is missing in residue CYM 117 in the pdb file
 You might need to add atom HN to the hydrogen database of building
block CYM
 in the file aminoacids.hdb (see the manual)


WARNING: atom HA is missing in residue CYM 117 in the pdb file
 You might need to add atom HA to the hydrogen database of building
block CYM/
/ in the file aminoacids.hdb (see the manual)


WARNING: atom HB1 is missing in residue CYM 117 in the pdb file
 You might need to add atom HB1 to the hydrogen database of building
block CYM
 in the file aminoacids.hdb (see the manual)


WARNING: atom HB2 is missing in residue CYM 117 in the pdb file
 You might need to add atom HB2 to the hydrogen database of building
block CYM
 in the file aminoacids.hdb (see the manual)


WARNING: atom O1 is missing in residue CYM 117 in the pdb file


---
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1463

Fatal error:
There were 10 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors/

I checked the .hdb file, but it seemed not to require hydrogen adding for
CYS. Moreover, the atoms of MTSL like "O1" are not protein atoms, and they
are described by CGenFF. Now some of them are missing . Can you give me the
solution? Thank you!

Qing Liu



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Re: [gmx-users] Tesla M2075 error...

[Justin Lemkul]

On 10/16/12 9:58 AM, Anthony Cruz Balberdi wrote:

Hi user:

I was able to compile gromacs with GPU support without errors, but when I
test it with the benchmark got the following error:

(mdrun-gpu -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no" -s topol.tpr
-v)

Fatal error:
The selected GPU (#0, Tesla M2075) is not supported by Gromacs! Most
probably you have a low-end GPU which would not perform well, or new
hardware that has not been tested with the current release. If you still
want to try using the device, use the force-device=yes option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

This is normal behaviour or I made something wrong in the configuration?
because is clear in the website that Tesla M2075 is supported by gromacs.
The only solution is changing force-device to yes?



Correct.  The list of supported GPU's is outdated in the code and should be 
fixed for the next release.


-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] Tesla M2075 error...

[Anthony Cruz Balberdi]

Hi user:

I was able to compile gromacs with GPU support without errors, but when I
test it with the benchmark got the following error:

(mdrun-gpu -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no" -s topol.tpr
-v)

Fatal error:
The selected GPU (#0, Tesla M2075) is not supported by Gromacs! Most
probably you have a low-end GPU which would not perform well, or new
hardware that has not been tested with the current release. If you still
want to try using the device, use the force-device=yes option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

This is normal behaviour or I made something wrong in the configuration?
because is clear in the website that Tesla M2075 is supported by gromacs.
The only solution is changing force-device to yes?

Thanks.

Anthony
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[gmx-users] Re: The problem of converting CGenff parameters to those of Gromacs

[spin]

Hi, Peter and David,

Thank you for your help! I have solve it by David's script.

Qing Liu



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Re: [gmx-users] OpenMM does not support -reg

[Justin Lemkul]

On 10/16/12 9:38 AM, venkatesh s wrote:

Respected gromacs people,
  while running mdrun-gpu -v -deffnm
nvt  Following error i got , I searched in net forums and  gmx-users
mailing list   but ..?
So Kindly provide solution for that  (grompp nvt step  i completed )



Program mdrun-gpu, VERSION 4.5.5
Source code file:
/opt/softwares/compile/gromacs-4.5.5/src/kernel/openmm_wrapper.cpp, line:
618

Fatal error:
OpenMM does not support (some) of the provided interaction type(s)
(Position Rest.)



You can't use position restraints when running on GPU.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] g_density, number density

[Justin Lemkul]

On 10/16/12 7:55 AM, Ali Alizadeh wrote:

Dear All users

1- When i use these commands for generating number density profile

I see completely different results(in z direction, length in z
direction is 8, number density versus of z)

g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z -symm -center

It's trend is increasing(from z=0 to z=2 then decreasing(fall to zero,
z= 2-5) and then increasing(z=5-7.5)

g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z

But in the case,It's trend is decreasing(z=0-2.5) then
increasing(suddenly to maximum, z=2.5-5) and then decreasing(z=5-8)



You're telling g_density to do two different things.  You got two different 
results.  I don't see that as odd.



2- Number density profile Should be symmetric?



Only if the system is symmetric.

-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] removal of water

[Justin Lemkul]

On 10/16/12 7:46 AM, Shine A wrote:

Sir,

I am studying the dynamics of membrane proteins using KALP-15 in DPPC.I
solvated  the system using

  genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro  .
But system_shrink1_solv.gro contain some unwanted water molecules in
between lipid. How to eliminate these water molecules?plz help.



You should not add water until the system is completely packed.  Otherwise you 
just end up with a system with a huge amount of atoms in incorrect locations.

Generally, one can remove unwanted waters rather easily:

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

But I would still suggest you re-evaluate your approach.

-Justin

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Research Scientist
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Re: [gmx-users] tpr file

[Justin Lemkul]

On 10/16/12 7:42 AM, ahmet yıldırım wrote:

Hi,

I converted a .tpr file to .pdb using editconf.
editconf -f md.tpr -o new-md.pdb
I visualised new-topol.pdb using pymol. It has the virtual sites.
Furthermore, the molecule(s) does not stay in the centre of the box.
I need a proper .tpr or .pdb file for analysis.
How can these problems fixed?



The "center" of a periodic system (assuming that's what you have) is arbitrary. 
 If you need some fixed reference, that's what trjconv -center does.


-Justin

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Research Scientist
Department of Biochemistry
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Re: [gmx-users] Load imbalance logging, how to limit it?

[Justin Lemkul]

On 10/16/12 1:02 AM, Ladasky wrote:

I'm getting control over my .mdp files, cutting down on the generation of
data for which I currently have no use.  I just changed the nstenergy
parameter to 2500 cycles, much larger than its default value of 100 cycles.
This reduced logging still gives me plenty of data for monitoring the
stability of long runs.

In my .log file, however, load imbalances are still being reported every 10
cycles.  Once in a while, I'll get a 15% to 20% load imbalance, but most of
the time it's under 2%.  It's nothing that I seem to need to worry about at
this time.  I would like to reduce the load imbalance reporting frequency as
well.  What is the .mdp file key word that accomplishes this?



nstlog controls log file output.

-Justin

--


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Research Scientist
Department of Biochemistry
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Re: [gmx-users] Re: amount of solvent

[Justin Lemkul]

On 10/15/12 8:59 PM, shika wrote:

Thanks all,

I already pack the mixed solvent by using packmol cause the box that i
used octahedron.Therefore the error that coming out is that topology
and the gro file does not
same. When I view the solvent by VMD  its just shows that the mixture
only fill in the cubic form even though the starting box that i need
was octahedron.
So I would like to ask you guys if I already pack all the molecule,i
need to create the new topology right? before start to minimize?



Since you need a topology to get a run input file, yes.  Your topology needs to 
match the coordinate file in terms of the number of each species present and the 
order in which they appear.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] how can I create gromos and top file for graphene

[Justin Lemkul]

On 10/15/12 5:53 PM, Yihua Zhou wrote:

Dear Sir/Madam

I am trying to use GROMACS to simulate DNA translocation through graphene
nanopore, however, I don’t know how to create the *.top and *.gro files for
my case, I know I can use pdb2gmx to obtain topology and gromos file for
DNA, but I don’t know how to obtain the necessary files for grapheme, could
you please give me some suggestions?



Some related advice:

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

-Justin

--


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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] removal of water

[Shine A]

Sir,

   I am studying the dynamics of membrane proteins using KALP-15 in DPPC.I
solvated  the system using

 genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro  .
But system_shrink1_solv.gro contain some unwanted water molecules in
between lipid. How to eliminate these water molecules?plz help.
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[gmx-users] tpr file

[ahmet yıldırım]

Hi,

I converted a .tpr file to .pdb using editconf.
editconf -f md.tpr -o new-md.pdb
I visualised new-topol.pdb using pymol. It has the virtual sites.
Furthermore, the molecule(s) does not stay in the centre of the box.
I need a proper .tpr or .pdb file for analysis.
How can these problems fixed?

Thanks in advance
--
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Re: [gmx-users] Problem with equilibrated lipid bilayer structure

[Thomas Piggot]

Hi Jernej,

You can have a look at our paper linked by both Peter and Sebastien 
earlier in this thread, which has a detailed methods section. 
Alternatively search in the GROMACS mailing list archives, as this has 
been discussed in detail before.


Cheers

Tom

Jernej Zidar wrote:

Hi Tom,
  Thanks for the detailed reply.

  Could you please suggest the appropriate cut-offs and/or parameters
I should use?

Thanks,
Jernej

On Mon, Oct 15, 2012 at 5:46 PM,   wrote:

Subject: Re: [gmx-users] Problem with equilibrated lipid bilayer
structure
To: Discussion list for GROMACS users 
Message-ID: <507bda00.8060...@soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

Hi Jernej,

The CHARMM force field was developed for use with the TIP3P model making
this probably the appropriate choice, even if this model may not perform
the best for simulations of pure water (see
http://pubs.acs.org/doi/abs/10.1021/jz200167q for some more details).

As for some specific GROMACS points with the CHARMM36 lipids. Firstly I
recommend you to use the CHARMM TIP3P variant and secondly you should
also be careful with the cut-off's you choose. I do not think a
dispersion correction would be appropriate and you should also probably
be using some different cut-off's to those you give in you mdp
(typically a switching off of the van der Waals interactions is done
with this force field). Finally you also need to be careful constraining
all bonds (instead of just bonds to hydrogen atoms) with this force
field. We found that we needed to increase the accuracy of the LINCS
settings when constraining all bonds to ensure energy conservation.

Cheers

Tom






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[gmx-users] Version 4.6

[SebastianWaltz]

Hey together,

I am wondering when the stable version of 4.6 will be released. I am
using the prerelease version for basic NVT and NPT full atom simulations
for months now with great success and wonder what is missing for the
full release. I would be very grateful for some informations about the
current status of the 4.6 version.

Thanks a lot

Sebastian
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