[gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

[Emma Eriksson]

Thank you David for your response. Please see my reply below. 

On 2012-10-04 11:50, Emma Eriksson wrote:
> Dear all,
>
> I am using the pull code in Gromacs 4.5.5 to constrain the distance in one 
> direction (z) between a small molecule and a lipid bilayer. I run separate 
> simulations with distances 0-4 nm constrained. I use pull_geometry = 
> cylinder. The pull parameters are the following:
>
> pull   = constraint
> pull_geometry   = cylinder
> pull_r1  = 1.0
> pull_r0  = 1.5
> pull_group0   = DMPC
> pull_group1   = 2
> pull_vec1  = 0 0 1
> pull_init1   = x
>
> I have previously been using the same methodology in 4.0.5 without problems. 
> When i run grompp in 4.5.5 I get the following error:
>
> Fatal error:
> Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size 
> (3.012310)
>
> The source of the first value, which should be the distance of pull group 1 
> is for me unknown. A value of ~4 is generated for all systems no matter what 
> z distance is actually betwen the two groups (0-4 nm), so the value has no 
> connection to the z distance between the groups. The second value is 0.5 
> times the x box length. I have read through pull.c, but I cannot find an 
> explanation to why the x direction seems to be considered and not the z 
> direction. When I run grompp with pull_geometry = distance or direction 
> together with pull_dim = N N Y there is no problem.
>
> As I am not sure of the source of this error when running with cylinder I do 
> not know if it is only related to the check or if the following simulation 
> would be affected if I uncomment the check.
>
> Any suggestions to why this is happening and what I can do about it?
> Check the other pull_XXX values in mdout.mdp
> You have not specified all of them above, e.g. pull_direction?

The pull parameter section in mdout.mdp are the following:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = constraint
; Pull geometry: distance, direction, cylinder or position
pull_geometry= cylinder
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1.0
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1.5
pull_constr_tol  = 1e-06
pull_start   = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0  = DMPC
pull_weights0=
pull_pbcatom0= 0
pull_group1  = 2
pull_weights1=
pull_pbcatom1= 0
pull_vec1= 0 0 1
pull_init1   = 0
pull_rate1   = 0
pull_k1  = 0
pull_kB1 = 0

I did not specify pull_dim as I understood it from the manual that this should 
not be used this for pull_geometry = cylinder (however, pull_dim will be set to 
the default Y Y Y in mdout.mdp). I specify pull_vec1 = 0 0 1, which should give 
the pull direction (z in this case). Did I misunderstand this somehow?

When I specify pull_dim = N N Y I do not get any error with grompp, but instead 
I obtain the following:

Pull group  natoms  pbc atom  distance at start reference at t=0
   0  5888  2944 
   149 20922   3.685 0   

The distance between the two groups should be 0 but the program interpret is as 
3.685, which is a value that I do not know where it comes from. 

I do not know what other options I can try or what is wrong here. Do you have 
any suggestion what is going on? Thank you.

Emma

> Thanks!
>
> Best regards,
> Emma --
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Re: [gmx-users] residue-residue interaction energies

[federico vaglio]

Hi Justin,
thank you for your quick reply.

When you say:

"..Probably by analyzing them individually with mdrun -rerun to recalculate
each frame.  Tedious, but can be easily scripted..."

do you mean I have to run g_enemat module using -b and -e options in order
to set the first and the last frame to read from trajectory?
If not, could you please suggest me the correct way to do so?

thank you again.

Federico

On Sat, Oct 6, 2012 at 4:54 AM, Justin Lemkul  wrote:

>
>
> On 10/5/12 1:40 PM, federico vaglio wrote:
>
>> Dear all,
>> I would like to extract the interaction energies (LJ
>> and electrostatic) between each residue pairs from my trajectory.
>> The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
>> LJ-SRemat.xpm, totalemat.xpm) but not a "data" file with
>> the residue-residue interaction energies I'm looking for.
>> Is there a way to get these numbers? Or have I to read the xpm "matrix"
>> and
>> convert all those letters to the corresponding energy values?
>>
>
> Yes, you have to map it out based on the .xpm labels.
>
>
>  Finally, is there a way to get pairwise residue-residue interaction energy
>> values from each snapshot of my trajectory ?
>>
>>
> Probably by analyzing them individually with mdrun -rerun to recalculate
> each frame.  Tedious, but can be easily scripted.
>
> -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] Re: DNA orientation restrain

[Tong Dudu]

Thanks, Erik.

Actually, I tried to use periodic molecules in my previous simulations. But
I think that can be only applied to DNA molecules of certain length, say
10bps, 20bps. But my DNA molecule here doesn't meet that criteria.

Dudu



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[gmx-users] Re: gmx-users Digest, Vol 102, Issue 45

[Kathleen Kirchner]

Dear Vitaly,

I had to struggle with the equilibration of an ionic liquid at charged 
electrodes - it means a spatial inhomogeneous system and high forces due 
to the electrostatics). I found the following tricks working for me:


* Pre-equilibration with a reduction of the step size (e.g. from 2 fs to 
0.2 fs): After a several thousands steps (depends on the system of 
course) the jobs can be restarted with the required time step simply by 
using the .gro output file.


* Reducing the temperature and slowly heating the system by annealing.

* Don't use "generate initial velocities"!

* Assigning zero charges to some particles for the first equilibration 
(E.g. in my case I had to charge the electrodes, which nearly always 
crashed if I didn't to an equilibration before hand with neutral 
electrodes. - Might be not useful in your case).


* Mixture of all steps above :)

I hope you will find some idea that helps you with the equilibration.

Regards
Kathleen


On 10/06/2012 07:27 PM, gmx-users-requ...@gromacs.org wrote:

Message: 3
Date: Sat, 6 Oct 2012 18:03:54 +0200
From: "Dr. Vitaly Chaban"
Subject: [gmx-users] domain decomposition trick for highly parallel
non-equilibrium runs
To:gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Dear all -

Would anyone perhaps suggest some tricks to increase the stability of
the highly parallel jobs (NP > 100), which use domain decomposition
among nodes. Especially, for the case, where beginning state of the
system is not equilibrium state (although it contains no bad contacts,
etc), i.e. the potential energy of the system decreases during MD.

Thank you for insights,
Vitaly Chaban

-- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics 
Department of Physics, Chemistry and Pharmacy University of Southern 
Denmark Campusvej 55, 5230 Odense M, Denmark


--
Kathleen Kirchner
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Leipzig
e-mail: kirch...@mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/
Tel +49 341 9959 725
Fax +49 341 9959 999

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[gmx-users] Re: Segmentation fault, mdrun_mpi

[Ladasky]

Justin Lemkul wrote
> My first guess would be a buggy MPI implementation.  I can't comment on
> hardware 
> specs, but usually the random failures seen in mdrun_mpi are a result of
> some 
> generic MPI failure.  What MPI are you using?

I am using the OpenMPI package, version 1.4.3.  It's one of three MPI
implementations which are included in the standard repositories of Ubuntu
Linux 11.10.  I can also obtain MPICH2 and gromacs-mpich without jumping
through too many hoops.  It looks like LAM is also available.  However, if
GROMACS needs a special package to interface with LAM, it's not in the
repositories.

Alternately, I could drop using the external MPI for now and just use the
new multi-threaded GROMACS defaults.  I was trying to prepare for longer
runs on a cluster, however.  If those runs are going to crash, I had better
know about it now.



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Re: [gmx-users] Re: DNA orientation restrain

[Erik Marklund]

Hi,

Yes. Although not applicable to all systems, as you correctly state, a slightly 
extended periodic DNA helix could still yield a smaller box since the 
non-periodic molecule would need a minimum distance to its periodic copy, the 
length of which depending on the non-bonded interactions. Hence, extending the 
helix by a few nucleotides could be worth it, depending on what you aim to 
study. On the other hand, neighbor searching is a bit slower when there are 
periodic molecules are present in the system, but I do not know how much of an 
effect that has on performance.

Best,

Erik

8 okt 2012 kl. 10.01 skrev Tong Dudu:

> Thanks, Erik.
> 
> Actually, I tried to use periodic molecules in my previous simulations. But
> I think that can be only applied to DNA molecules of certain length, say
> 10bps, 20bps. But my DNA molecule here doesn't meet that criteria.
> 
> Dudu
> 
> 
> 
> --
> View this message in context: 
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---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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[gmx-users] how to center the protein?

[Albert]

Dear:

  I am using the command:

trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol

trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans

to extract a frame of my md simulation and I found my protein is not in 
the centre of simulation box. here is a figure for it:



https://dl.dropbox.com/u/56271062/position.jpg

as we cab see the protein is just in the corner of box and the water 
molecules (lefft sphere) in the protein was separate from protein and on 
the otherside of box.


THX
Albert
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Re: [gmx-users] Interaction energy..

[rama david]

Hi justin,
As per your advice,

 g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???

thank you in advance.


With best wishes and regards
Rama david.






On Sat, Oct 6, 2012 at 6:47 PM, Justin Lemkul  wrote:

>
>
> On 10/6/12 6:26 AM, rama david wrote:
>
>> Hi justin,
>>
>> I tried as per your suggestion.
>>
>> command line
>>
>> g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free
>>
>> the out put is like ,
>>
>>
>>
>> Opened ener.edr as single precision energy file
>> Will read groupnames from inputfile
>> Read 2 groups
>> group 0WARNING! could not find group (null):energy-energy (0,0)in energy
>> file
>> WARNING! could not find group (null):energy-extra34 (0,1)in energy file
>> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
>> file
>>
>> Will select half-matrix of energies with 3 elements
>> Last energy frame read 5 time 1.000
>> Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
>> Segmentation fault (core dumped)
>>
>> why program not work ?? Is it  bug??? or Am I doing any stupid mistake???
>>
>>
> It might be a bug, but I'm not sure yet.  Please run the command without
> the -free option (and thus without -temp) to further reduce complexity.
>  Then manually add the -coul flag.  It should be set by default, but at
> this point the screen output seems to indicate that no energy terms are
> being detected.
>
>
> -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] how to center the protein?

[rama david]

HI

you can put the protein in center by adding flag -center to trjconv ( see
trjconv -h)

use the proper index file ( if you made ) -n ..

You can also use the -pbc cluster and extract the specific time frame by
flag  -dump

see trjconv very carefully ,It has  the way to do it.


With best wishes and regards
Rama david


On Mon, Oct 8, 2012 at 3:06 PM, Albert  wrote:

> Dear:
>
>   I am using the command:
>
> trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol
>
> trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans
>
> to extract a frame of my md simulation and I found my protein is not in
> the centre of simulation box. here is a figure for it:
>
>
> https://dl.dropbox.com/u/**56271062/position.jpg
>
> as we cab see the protein is just in the corner of box and the water
> molecules (lefft sphere) in the protein was separate from protein and on
> the otherside of box.
>
> THX
> Albert
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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/8/12 5:40 AM, rama david wrote:

Hi justin,
As per your advice,

  g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???



I told you to add the -coul flag, not -nocoul.  With the above command, you're 
explicitly telling g_enemat to not do anything useful.


-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] Interaction energy..

[rama david]

Hi justin,
I correct command as follow and
 g_enemat -f ener.edr -groups groups.dat -coul -lj

out-put is like


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 9 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames
Segmentation fault (core dumped)


On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul  wrote:

>
>
> On 10/8/12 5:40 AM, rama david wrote:
>
>> Hi justin,
>>
>> As per your advice,
>>
>>   g_enemat -f ener.edr -groups groups.dat -nocoul -nolj
>>
>>
>> Opened ener.edr as single precision energy file
>> Will read groupnames from inputfile
>> Read 2 groups
>> group 0WARNING! could not find group (null):energy-energy (0,0)in energy
>> file
>> WARNING! could not find group (null):energy-extra34 (0,1)in energy file
>> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
>> file
>>
>> Will select half-matrix of energies with 0 elements
>> Last energy frame read 5 time 1.000
>> Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
>> Segmentation fault (core dumped)
>>
>> What is the reason  ???
>>
>>
> I told you to add the -coul flag, not -nocoul.  With the above command,
> you're explicitly telling g_enemat to not do anything useful.
>
>
> -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] Interaction energy..

[Justin Lemkul]

On 10/8/12 6:00 AM, rama david wrote:

Hi justin,
I correct command as follow and
  g_enemat -f ener.edr -groups groups.dat -coul -lj

out-put is like


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 9 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames
Segmentation fault (core dumped)



Let me be a bit more specific again.  I previously suggested there was a problem 
with the -lj flag activating more than one option in the code, so that is a 
potential problem.  I suggested adding -nolj -coul to test this theory.  Please 
use those options (not -coul -lj) and see what happens.


-Justin



On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul  wrote:




On 10/8/12 5:40 AM, rama david wrote:


Hi justin,

As per your advice,

   g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???



I told you to add the -coul flag, not -nocoul.  With the above command,
you're explicitly telling g_enemat to not do anything useful.


-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: Segmentation fault, mdrun_mpi

[Justin Lemkul]

On 10/8/12 4:39 AM, Ladasky wrote:

Justin Lemkul wrote

My first guess would be a buggy MPI implementation.  I can't comment on
hardware
specs, but usually the random failures seen in mdrun_mpi are a result of
some
generic MPI failure.  What MPI are you using?


I am using the OpenMPI package, version 1.4.3.  It's one of three MPI
implementations which are included in the standard repositories of Ubuntu
Linux 11.10.  I can also obtain MPICH2 and gromacs-mpich without jumping
through too many hoops.  It looks like LAM is also available.  However, if
GROMACS needs a special package to interface with LAM, it's not in the
repositories.



This all seems reasonable.  I asked about the MPI implementation because people 
have previously reported that using LAM (which is really outdated) causes random 
seg faults and errors.  I would not necessarily implicate OpenMPI, as I use it 
routinely.  I never use repositories (I always compile from source) as I have 
gotten buggy packages in the past, but I don't know if that's relevant here or 
not.  I'm not trying to implicate the package maintainer in any way, just noting 
that long ago (5-6 years) the Gromacs package had some issues.


-Justin


Alternately, I could drop using the external MPI for now and just use the
new multi-threaded GROMACS defaults.  I was trying to prepare for longer
runs on a cluster, however.  If those runs are going to crash, I had better
know about it now.



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Re: [gmx-users] residue-residue interaction energies

[Justin Lemkul]

On 10/8/12 3:14 AM, federico vaglio wrote:

Hi Justin,
thank you for your quick reply.

When you say:

"..Probably by analyzing them individually with mdrun -rerun to recalculate
each frame.  Tedious, but can be easily scripted..."

do you mean I have to run g_enemat module using -b and -e options in order
to set the first and the last frame to read from trajectory?
If not, could you please suggest me the correct way to do so?



Not what I was suggesting, but using -b and -e should also work.

-Justin


thank you again.

Federico

On Sat, Oct 6, 2012 at 4:54 AM, Justin Lemkul  wrote:




On 10/5/12 1:40 PM, federico vaglio wrote:


Dear all,
I would like to extract the interaction energies (LJ
and electrostatic) between each residue pairs from my trajectory.
The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
LJ-SRemat.xpm, totalemat.xpm) but not a "data" file with
the residue-residue interaction energies I'm looking for.
Is there a way to get these numbers? Or have I to read the xpm "matrix"
and
convert all those letters to the corresponding energy values?



Yes, you have to map it out based on the .xpm labels.


  Finally, is there a way to get pairwise residue-residue interaction energy

values from each snapshot of my trajectory ?



Probably by analyzing them individually with mdrun -rerun to recalculate
each frame.  Tedious, but can be easily scripted.

-Justin

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Re: [gmx-users] Re: Fwd: How to can i replace a molecule

[Justin Lemkul]

On 10/8/12 12:48 AM, shika wrote:

it is because when i put

genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top
-o prot_solv.gro

the error turn out like this :

System total charge: 0.000
Grid: 17 x 16 x 14 cells
nri = 12718, nrj = 100152
Try 9119box_margin = 0.45overlap:
Killed

thats why i need to run genbox twice



Sorry, read the original message too quickly and thought the solvent 
configuration was the same both times.  My mistake :)


The error you receive is a result of genbox failing to do what you're asking. 
You've exhausted the memory available, suggesting that there is no way to add 
that many molecules of whatever solvent into the box.  Either set a larger box 
with editconf prior to this step, or try to insert fewer molecules.


-Justin


On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS]
 wrote:



On 10/7/12 9:17 PM, shika wrote:


Thanks Justin.

May I ask something, if i'm using the command for genbox before
minimization which is

genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro

next i insert water by using same command;

genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o
prot_solv_wtr.gro maxsol 350

i'm using -cs for both genbox command instead of -ci -nmol, is it
wrong to use the command like that?




I don't understand why you need two invocations of genbox, but syntactically
the
commands are correct.  The -ci -nmol options are for adding molecules
randomly
in the unit cell.  The -cs option is for stacking grids of water boxes (or
whatever other solvent you provide) within the unit cell.

-Justin




On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
<[hidden email]> wrote:



On 10/7/12 3:52 PM, Ali Alizadeh wrote:

Dear All users

How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,

Can I use genbox or genion, How to do i do it?



Likely you can't, as you were already advised:

http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html

A more robust approach for dealing with mixed systems can be found here:

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

-Justin

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Re: [gmx-users] Interaction energy..

[rama david]

Hi justin,


g_enemat -f ener.edr -groups groups.dat -coul -nolj


Out-put is like

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)


Thank you in advance
Rama david.

>
>>
> Let me be a bit more specific again.  I previously suggested there was a
> problem with the -lj flag activating more than one option in the code, so
> that is a potential problem.  I suggested adding -nolj -coul to test this
> theory.  Please use those options (not -coul -lj) and see what happens.
>
> -Justin
>
>
>> On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 10/8/12 5:40 AM, rama david wrote:
>>>
>>>  Hi justin,

 As per your advice,

g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


 Opened ener.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):energy-energy (0,0)in energy
 file
 WARNING! could not find group (null):energy-extra34 (0,1)in energy file
 group 1WARNING! could not find group (null):extra34-extra34 (1,1)in
 energy
 file

 Will select half-matrix of energies with 0 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
 Segmentation fault (core dumped)

 What is the reason  ???


  I told you to add the -coul flag, not -nocoul.  With the above command,
>>> you're explicitly telling g_enemat to not do anything useful.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
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>>>
>>>
> --
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>
> Justin A. Lemkul, Ph.D.
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> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
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> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/8/12 7:09 AM, rama david wrote:

Hi justin,


g_enemat -f ener.edr -groups groups.dat -coul -nolj


Out-put is like

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)



At this point, I honestly have no idea why it's not working.  If you want me to 
try to debug the issue a bit, you can send me the .edr file (off-list) if it can 
be sent via email.  If it is too large of a file, use eneconv to cut down some 
frames.


-Justin

--


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Department of Biochemistry
Virginia Tech
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[gmx-users] Re: domain decomposition trick for highly parallel, non-equilibrium runs

[Kathleen Kirchner]

Sorry for double post, first message had the wrong subject.

Dear Vitaly,

I had to struggle with the equilibration of an ionic liquid at charged
electrodes - it means a spatial inhomogeneous system and high forces due
to the electrostatics). I found the following tricks working for me:

* Pre-equilibration with a reduction of the step size (e.g. from 2 fs to
0.2 fs): After a several thousands steps (depends on the system of
course) the jobs can be restarted with the required time step simply by
using the .gro output file.

* Reducing the temperature and slowly heating the system by annealing.

* Don't use "generate initial velocities"!

* Assigning zero charges to some particles for the first equilibration
(E.g. in my case I had to charge the electrodes, which nearly always
crashed if I didn't to an equilibration before hand with neutral
electrodes. - Might be not useful in your case).

* Mixture of all steps above :)

I hope you will find some idea that helps you with the equilibration.

Regards
Kathleen


On 10/06/2012 07:27 PM, gmx-users-requ...@gromacs.org wrote:

Message: 3
Date: Sat, 6 Oct 2012 18:03:54 +0200
From: "Dr. Vitaly Chaban"
Subject: [gmx-users] domain decomposition trick for highly parallel
non-equilibrium runs
To:gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Dear all -

Would anyone perhaps suggest some tricks to increase the stability of
the highly parallel jobs (NP > 100), which use domain decomposition
among nodes. Especially, for the case, where beginning state of the
system is not equilibrium state (although it contains no bad contacts,
etc), i.e. the potential energy of the system decreases during MD.

Thank you for insights,
Vitaly Chaban

-- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy University of Southern
Denmark Campusvej 55, 5230 Odense M, Denmark


--
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Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Leipzig
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[gmx-users] Re: gmx-users Digest, Vol 102, Issue 52

[Ali Alizadeh]

Dear usres

Thank you for your replies

1- Is it possible define a ion as a propane molecule and then
I do adding propane molecules instead of methane molecules in my system?

2- Other wise, I select 300 molecules  of methane and remove them from my
system(randomly and by hand, for example 500 molecules of methane and
adding 100 molecules of propane,)
[Dr. Vitaly Chaban comment]

Is it possible and common method?


I am using OPLS AA ff,

Sincerely
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Re: [gmx-users] domain decomposition trick for highly parallel non-equilibrium runs

[Bogdan Costescu]

On Sat, Oct 6, 2012 at 6:03 PM, Dr. Vitaly Chaban  wrote:
> Would anyone perhaps suggest some tricks to increase the stability of
> the highly parallel jobs (NP > 100), which use domain decomposition
> among nodes.

It would be more helpful to know what you are talking about, i.e. a
definition of stability (or maybe of instability, which you probably
try to avoid)...

Cheers,
Bogdan
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[gmx-users] Re: pull=constraint gives zero forces

[alex.bjorling]

Following up on this post. I've tried the same runs using version 4.0.7,
which gave immediate segmentation faults. Not sure if this is a clue or a
trivial consequence of switching versions, but there it is.

Any other ideas why the pullf output just contains zeros?

Cheers,
Alex


alex.bjorling wrote
> I'm using the pull code to maintain the initial structure of a protein
> that otherwise deforms. Using pull=umbrella does what I expect it to,
> but pull=constraint produces zero forces. I'm using version 4.5.5 with
> the MARTINI force field.
> 
> The pull=umbrella mdp contains the following,

> 
> and gives the following pullf output:

> 
> For such runs, the group COM:s stay within 0.1 nm of their initial
> positions, throughout a long trajectory.
> 
> The pull=constraint mdp starts with

> 
> and produces the pullf output

> 
> For these runs, the group COM:s move around freely. I guess I'm doing
> something wrong but can't work out what. I've tried specifying k:s for
> the contraint runs, and tried removing all other constraints in the
> molecule. I've tried to comply with the manual's instructions but to
> no avail.
> 
> Any ideas?
> 
> Cheers,
> Alexander Björling,
> PhD candidate, University of Gothenburg, Sweden





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[gmx-users] About Lincs Algorithim for Cyclic Peptide

[vidhya sankar]

Dear Justin Thank you For your Previous reply

   I have used the EM.gro file of Cyclic Peptide  For NPT Equlibrartion Without 
using  Lincs Algorithim it run Suceesfully 
But with Lincs Algorithm It shows Errror As follows Though  I have reduce the 
time step   
 
relative constraint deviation after LINCS:
rms 3069855679.355833, max 11186146428.941977 (between atoms 164 and 165)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    166    167  143.7    0.1935 179340257.0542  0.1530
    166    167  143.7    0.1935 179340257.0542  0.1530
    168    169  158.7    1.4560 636653487.7409  0.1230
    168    169  158.7    1.4560 636653487.7409  0.1230
    164    168  171.7    2.0007 1704071509.3304  0.1530
    164    165  169.7    1.8838 1711480403.7811  0.1530
    164    168  171.7    2.0007 1704071509.3304  0.1530
    164    165  169.7    1.8838 1711480403.7811  0.1530
    165    166  165.2    0.6922 762944969.2944  0.1530
    165    166  165.2    0.6922 762944969.2944  0.1530
  1  2  139.5    0.1011 1465776.5396  0.1000
  1    168  169.4    1.1190 546331954.5273  0.1330
    145    147   38.1    0.1330   0.1781  0.1330
   
step 0: Water molecule starting at atom 7265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#
Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Segmentation fault

  Normally The Gromacs Does Not Have terminal option for cyclic Peptide While 
constructing  .top for Cyclic Peptide (By using pdb2gmx) As Advised By mark I  
Have Edited My  initial pdb file final .top file compatible to cyclic Peptide 
(by Making Bond  between first and Last residue And then Making proper 
angle,Dihedral and other factors)  
Now I am confident on that topology . Also Bond Between First and Last Residue 
Are Intact throughout  Entire Dynamics ( Here I am Running Without Lincs 
Algorithm)

My Question is
  Is it Reasonable and Meaningful To equilibrate And  do Production MD  Without 
Lincs  otherwise 
Is My EM  Not well Enough ? Because I am doing Three Cycles of EM Output is as 
follows
Steepest Descents converged to Fmax < 6800 in 2 steps
Potential Energy  = -2.08749539864389e+05
Maximum force =  6.52976950643761e+03 on atom 17042
Norm of force =  4.52145850945473e+02 
But When I Equilibrate With Lincs still  It Shows Bad contacts As Mentioned 
Above  


My NPT.mdp file are as follows
title   = NPT Equilibration 
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md    ; leap-frog integrator
nsteps  = 10    ; 2 * 5 = 100 ps
dt  = 0.0002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation = no    ; Initial simulation 
constraint_algorithm = lincs ; holonomic constraints 
constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
;lincs_iter   = 1 ; accuracy of LINCS
;lincs_order  = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4   ; short-range electrostatic cutoff (in nm)
rvdw    = 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; Weak coupling for initial equilibration 
tc-grps = Protein   Non-Protein ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 310   310 ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = isotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure (in bar)
compressibility = 4.5e-5    ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp    = 310

Re: [gmx-users] About Lincs Algorithim for Cyclic Peptide

[David van der Spoel]

On 2012-10-08 17:17, vidhya sankar wrote:

Dear Justin Thank you For your Previous reply

I have used the EM.gro file of Cyclic Peptide  For NPT Equlibrartion 
Without using  Lincs Algorithim it run Suceesfully
But with Lincs Algorithm It shows Errror As follows Though  I have reduce the 
time step



set lincs_iter = 2


relative constraint deviation after LINCS:
rms 3069855679.355833, max 11186146428.941977 (between atoms 164 and 165)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 166167  143.70.1935 179340257.0542  0.1530
 166167  143.70.1935 179340257.0542  0.1530
 168169  158.71.4560 636653487.7409  0.1230
 168169  158.71.4560 636653487.7409  0.1230
 164168  171.72.0007 1704071509.3304  0.1530
 164165  169.71.8838 1711480403.7811  0.1530
 164168  171.72.0007 1704071509.3304  0.1530
 164165  169.71.8838 1711480403.7811  0.1530
 165166  165.20.6922 762944969.2944  0.1530
 165166  165.20.6922 762944969.2944  0.1530
   1  2  139.50.1011 1465776.5396  0.1000
   1168  169.41.1190 546331954.5273  0.1330
 145147   38.10.1330   0.1781  0.1330

step 0: Water molecule starting at atom 7265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#
Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Segmentation fault

   Normally The Gromacs Does Not Have terminal option for cyclic Peptide While 
constructing  .top for Cyclic Peptide (By using pdb2gmx) As Advised By mark I  
Have Edited My  initial pdb file final .top file compatible to cyclic Peptide 
(by Making Bond  between first and Last residue And then Making proper 
angle,Dihedral and other factors)
Now I am confident on that topology . Also Bond Between First and Last Residue 
Are Intact throughout  Entire Dynamics ( Here I am Running Without Lincs 
Algorithm)

My Question is
   Is it Reasonable and Meaningful To equilibrate And  do Production MD  
Without Lincs  otherwise
Is My EM  Not well Enough ? Because I am doing Three Cycles of EM Output is as 
follows
Steepest Descents converged to Fmax < 6800 in 2 steps
Potential Energy  = -2.08749539864389e+05
Maximum force =  6.52976950643761e+03 on atom 17042
Norm of force =  4.52145850945473e+02
But When I Equilibrate With Lincs still  It Shows Bad contacts As Mentioned 
Above


My NPT.mdp file are as follows
title   = NPT Equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 10; 2 * 5 = 100 ps
dt  = 0.0002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation = no; Initial simulation
constraint_algorithm = lincs ; holonomic constraints
constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
;lincs_iter   = 1 ; accuracy of LINCS
;lincs_order  = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; Weak coupling for initial equilibration
tc-grps = Protein   Non-Protein ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 310   310 ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = isotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure (in bar)
compressibility = 4.5e-5; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes  

Re: [gmx-users] About Lincs Algorithim for Cyclic Peptide

[Justin Lemkul]

On 10/8/12 11:17 AM, vidhya sankar wrote:

Dear Justin Thank you For your Previous reply

I have used the EM.gro file of Cyclic Peptide  For NPT Equlibrartion 
Without using  Lincs Algorithim it run Suceesfully
But with Lincs Algorithm It shows Errror As follows Though  I have reduce the 
time step

relative constraint deviation after LINCS:
rms 3069855679.355833, max 11186146428.941977 (between atoms 164 and 165)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 166167  143.70.1935 179340257.0542  0.1530
 166167  143.70.1935 179340257.0542  0.1530
 168169  158.71.4560 636653487.7409  0.1230
 168169  158.71.4560 636653487.7409  0.1230
 164168  171.72.0007 1704071509.3304  0.1530
 164165  169.71.8838 1711480403.7811  0.1530
 164168  171.72.0007 1704071509.3304  0.1530
 164165  169.71.8838 1711480403.7811  0.1530
 165166  165.20.6922 762944969.2944  0.1530
 165166  165.20.6922 762944969.2944  0.1530
   1  2  139.50.1011 1465776.5396  0.1000
   1168  169.41.1190 546331954.5273  0.1330
 145147   38.10.1330   0.1781  0.1330

step 0: Water molecule starting at atom 7265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#
Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Segmentation fault

   Normally The Gromacs Does Not Have terminal option for cyclic Peptide While 
constructing  .top for Cyclic Peptide (By using pdb2gmx) As Advised By mark I  
Have Edited My  initial pdb file final .top file compatible to cyclic Peptide 
(by Making Bond  between first and Last residue And then Making proper 
angle,Dihedral and other factors)
Now I am confident on that topology . Also Bond Between First and Last Residue 
Are Intact throughout  Entire Dynamics ( Here I am Running Without Lincs 
Algorithm)

My Question is
   Is it Reasonable and Meaningful To equilibrate And  do Production MD  
Without Lincs  otherwise
Is My EM  Not well Enough ? Because I am doing Three Cycles of EM Output is as 
follows
Steepest Descents converged to Fmax < 6800 in 2 steps
Potential Energy  = -2.08749539864389e+05
Maximum force =  6.52976950643761e+03 on atom 17042
Norm of force =  4.52145850945473e+02
But When I Equilibrate With Lincs still  It Shows Bad contacts As Mentioned 
Above



Your system is insufficiently minimized, a value of Fmax < 1000 is generally 
acceptable for most protein-in-water systems.  Probably you have a bad starting 
geometry that is being forced to do something nasty when you impart a bond 
between the termini.  In any case, you can find out by visualization what atom 
17042 is and what its problem might be.


-Justin



My NPT.mdp file are as follows
title   = NPT Equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 10; 2 * 5 = 100 ps
dt  = 0.0002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation = no; Initial simulation
constraint_algorithm = lincs ; holonomic constraints
constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
;lincs_iter   = 1 ; accuracy of LINCS
;lincs_order  = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; Weak coupling for initial equilibration
tc-grps = Protein   Non-Protein ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 310   310 ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = isotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0   ; time constant, 

Re: [gmx-users] Unable to fire-up the parallel processes on cluster

[Justin Lemkul]

On 10/8/12 10:08 AM, Venkat Reddy wrote:

Dear Gromacs users,
I am trying to invoke a parallel job on three nodes (i101,i102,i103) using
the command as given in gromacs manual
mpirun -p i101,i102,i103 8 mdrun_mpi -v -s npt_100.tpr -deffnm npt_100

but its giving me an error like:
mpirun was unable to launch the specified application as it could not find
an executable:

Executable: -p

Please help me in this regard



Consult your MPI documentation for invocation options.  This is not a Gromacs 
problem.


-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: gmx-users Digest, Vol 102, Issue 52

[Justin Lemkul]

On 10/8/12 7:48 AM, Ali Alizadeh wrote:

Dear usres

Thank you for your replies

1- Is it possible define a ion as a propane molecule and then
I do adding propane molecules instead of methane molecules in my system?



Unlikely.


2- Other wise, I select 300 molecules  of methane and remove them from my
system(randomly and by hand, for example 500 molecules of methane and
adding 100 molecules of propane,)
[Dr. Vitaly Chaban comment]

 Is it possible and common method?



I think the best approach is contained in the link I already posted.  Place 
within whatever number of molecules of the minor species (propane) you want in 
the box, and then "solvate" with the major species (methane).


-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] I want to add 460 molecules into a box

[Justin Lemkul]

On 10/8/12 2:49 PM, Ali Alizadeh wrote:

Dear users

I want to add 460 molecules into a box but i can not add more than 400
molecules,

genbox -ci het.gro -nmol 460 -box ...

Even, when i change VanderWaals radii( i reduce it,vdwwradii.dat ) but
maximum molecules to be 440.

Decrease more than it, atoms overlap,

How to can i add my number of molecules(460) into system?



Use a bigger box.

-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] Gromacs-CPMD ....versions???

[raghav singh]

Hello Fellow Users,

I wanted to know about the gromacs versions compatible with interfacing
...with CPMD QM/MM...???

is that particular version provided by Dr. Biswas is the only one or the
latest versions are also capable of doing so???

Any News or info..or way???

Thank you all

cheers
Raghav
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[gmx-users] Re: domain decomposition trick for highly parallel, non-equilibrium runs

[Christopher Neale]

Dear Kathleen:

It is important to either load velocities or generate them. If you do neither, 
then initial forces will rapidly be scaled up to thermally appropriate 
velocities, and if the initial forces are concerted, then you can get 
significant undesired concerted motion that can do things like partially unfold 
a protein.

Chris.

-- original message --

Dear Vitaly,

I had to struggle with the equilibration of an ionic liquid at charged
electrodes - it means a spatial inhomogeneous system and high forces due
to the electrostatics). I found the following tricks working for me:

* Pre-equilibration with a reduction of the step size (e.g. from 2 fs to
0.2 fs): After a several thousands steps (depends on the system of
course) the jobs can be restarted with the required time step simply by
using the .gro output file.

* Reducing the temperature and slowly heating the system by annealing.

* Don't use "generate initial velocities"!

* Assigning zero charges to some particles for the first equilibration
(E.g. in my case I had to charge the electrodes, which nearly always
crashed if I didn't to an equilibration before hand with neutral
electrodes. - Might be not useful in your case).

* Mixture of all steps above :)

I hope you will find some idea that helps you with the equilibration.

Regards
Kathleen

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[gmx-users] Re: pull=constraint gives zero forces

[Christopher Neale]

Please post your entire .mdp file and a snip of the output in your pullf and 
pullc files.
(Your initial post on this topic was also missing these, although the text 
reads as if you intended to include them).

I'll note that there are no forces when using constraints, so the fact that you 
get zero forces for a constrained run
is not really surprising. I guess the thing is that it doesn't work to keep 
atoms in place for you, 
which we can help you with if you post more details.

Chris.

-- original message --

Following up on this post. I've tried the same runs using version 4.0.7,
which gave immediate segmentation faults. Not sure if this is a clue or a
trivial consequence of switching versions, but there it is.

Any other ideas why the pullf output just contains zeros?

Cheers,
Alex

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[gmx-users] (no subject)

[yp sun]

Dear all, 


When I try to install gromacs-4.5.5 on my centos system, I meet trouble. I 
installed fftw-3.3.2 and then install gromacs-4.5.5. When I type /.configure 
command, I got the error information: 

checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... 
configure: error: in `/gromacs/gromacs-4.5.5':
configure: error: C compiler cannot create executables
See `config.log' for more details.


The content of the config.log is the as following:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by gromacs configure 4.5.5, which was
generated by GNU Autoconf 2.64.  Invocation command line was

  $ ./configure --disable-float --prefix=/gromacs/gromacs-4.5.5

## - ##
## Platform. ##
## - ##

hostname = localhost.localdomain
uname -m = i686
uname -r = 2.6.18-308.el5
uname -s = Linux
uname -v = #1 SMP Tue Feb 21 20:05:41 EST 2012

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch  = i686
/usr/bin/arch -k   = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo  = unknown
/bin/machine   = unknown
/usr/bin/oslevel   = unknown
/bin/universe  = unknown

PATH: /usr/kerberos/sbin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/X11R6/bin
PATH: /home/sunyp/bin


## --- ##
## Core tests. ##
## --- ##

configure:3028: checking build system type
configure:3042: result: i686-pc-linux-gnu
configure:3062: checking host system type
configure:3075: result: i686-pc-linux-gnu
configure:3112: checking for a BSD-compatible install
configure:3180: result: /usr/bin/install -c
configure:3191: checking whether build environment is sane
configure:3241: result: yes
configure:3382: checking for a thread-safe mkdir -p
configure:3421: result: /bin/mkdir -p
configure:3434: checking for gawk
configure:3450: found /usr/bin/gawk
configure:3461: result: gawk
configure:3472: checking whether make sets $(MAKE)
configure:3494: result: yes
configure:3569: checking how to create a ustar tar archive
configure:3582: tar --version
tar (GNU tar) 1.15.1
configure:3585: $? = 0
configure:3625: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" 
>conftest.tar
configure:3628: $? = 0
configure:3632: tar -xf - &5
cc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-52)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:4386: $? = 0
configure:4375: cc -v >&5
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
--infodir=/usr/share/info --enable-shared --enable-threads=posix 
--enable-checking=release --with-system-zlib --enable-__cxa_atexit 
--disable-libunwind-exceptions --enable-libgcj-multifile 
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk 
--disable-dssi --disable-plugin 
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic 
--host=i386-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)
configure:4386: $? = 0
configure:4375: cc -V >&5
cc: '-V' option must have argument
configure:4386: $? = 1
configure:4375: cc -qversion >&5
cc: unrecognized option '-qversion'
cc: no input files
configure:4386: $? = 1
configure:4408: checking for C compiler default output file name
configure:4430: cc  /gromacs/fftw-3.3.2/include  conftest.c  >&5
/gromacs/fftw-3.3.2/include: file not recognized: Is a directory
collect2: ld returned 1 exit status
configure:4434: $? = 1
configure:4471: result: 
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.5"
| #define PACKAGE_STRING "gromacs 4.5.5"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.5"
| #define GMX_DOUBLE /**/
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Mon Oct  8 18:32:11 PDT 2012"
| #define BUILD_USER "root@localhost.localdomain"
| #define BUILD_MACHINE "Linux 2.6.18-308.el5 i686"
| /* end confdefs.h.  */
| #include 
| int
| main ()
| {
| FILE *f = fopen ("conftest.out", "w");
|  return ferror (f) || fclose (f) != 0;
| 
|   ;
|   return 0;
| }
configure:4477: error: in `/gromacs/gromacs-4.5.5':
configure:4481: error: C compiler cannot create executables
See `c

[gmx-users] distance between protein and ligand

[Archana Sonawani]

Hi,

I have simulated a protein-ligand complex for 5ns. I checked distance
between the important residues of protein and the ligand using g_dist. My
question is can the distance between the two groups decrease  from the
initial distance (docked complex as starting structure for simulation). I
know it may increase or may remain same at the end of the simulation.

for example: starting distance is 0.77nm and final distance is 0.8nm but
the intermediate course of simulation (around 3ns) it has decreased upto
0.65. The complex shows stability after 2ns. While the SASA between the two
groups is around 6.3 nm2  throughout the simulation which is very high.

This is very contradicting result. Is something wrong in the simulation?

Thanks in advance.

-- 
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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[gmx-users] generation of .itp file

[Shine A]

sir,

 I want to generate .itp from a pdb file. Is there any option in
gromacs.
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Re: [gmx-users] Re: pull=constraint gives zero forces

[Jaakko Uusitalo]

Hi Alex,

constraint pulling has a bug in 4.5.5, see: 
http://redmine.gromacs.org/issues/825. I'm guessing that's causing your 
problems. Fixing it is very easy (see the link) or you can also use an 
earlier version like 4.5.3 that works.


Best,
Jaakko

On 9.10.12 2:26 , Christopher Neale wrote:

Please post your entire .mdp file and a snip of the output in your pullf and 
pullc files.
(Your initial post on this topic was also missing these, although the text 
reads as if you intended to include them).

I'll note that there are no forces when using constraints, so the fact that you 
get zero forces for a constrained run
is not really surprising. I guess the thing is that it doesn't work to keep 
atoms in place for you,
which we can help you with if you post more details.

Chris.

-- original message --

Following up on this post. I've tried the same runs using version 4.0.7,
which gave immediate segmentation faults. Not sure if this is a clue or a
trivial consequence of switching versions, but there it is.

Any other ideas why the pullf output just contains zeros?

Cheers,
Alex



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