RE: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

[Berk Hess]

Hi,

I quickly ran the tpr file you provided on bugzilla, but I don't see an 
enormous energy drift.
What do you mean with "the energy explodes"?

Berk

Date: Wed, 21 Apr 2010 11:18:53 -0400
Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve   
simiulations
From: jampa...@gmail.com
To: gmx-users@gromacs.org

Dear Berk,
I am sorry for poor communication, Herewith i am giving my md.mdp file. I this 
file as you could see i am using two temp coupling groups Tmp1 is protein and a 
2nm spherical layer of water around it, and the second one Tmp2 which has only 
water. Now i want to fix the Tmp2 and apply 0 K to it. As you could see that 
from the file below i have taken Tcoupl  = V-rescale and two coupling 
groups Tmp1 and Tmp2 to make a frozen wall. I am not accelerating any group 
here.

In other words the goal of simulation is to check the behavior of protein is a 
confined sphere, i am trying to make frozen wall by freezing water around the 
protein after a specified distance. 


title   = SS2130cpp = 
/usr/bin/cppconstraints = all-bondsintegrator  = md
dt  = 0.002 ; ps !nsteps  = 100 nstxout = 
1000nstvout = 1000nstfout = 0nstlog  = 0nstenergy   
= 1000
nstlist = 5ns_type = gridrlist   = 1.0coulombtype = 
PMErcoulomb= 1.0rvdw= 1.0rvdw_switch = 0.9
fourierspacing  = 0.12fourier_nx  = 0fourier_ny  = 0fourier_nz  = 
0pme_order   = 4ewald_rtol  = 1e-5optimize_fft= yes
Tcoupl  = V-rescaletau_t   = 0.1  0.1tc-grps = Tmp1 
Tmp2ref_t   = 283.00.0gen_vel = yesgen_temp= 
283.0
gen_seed= 181726freezegrps  = Tmp2freezedim   = Y Y 
Y

Thanks very muchSrinivas.

On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess  wrote:






Hi,

I moved this to the user list, so it will be of use to others.

I have no clue what you are trying to do, what groups you are accelerating or 
freezing.
So we can't help you without further information.

Setting up simulations with frozen groups, accelerate groups or different 
coupling
temperatures is tricky and will in most cases destroy energy conservation.

Berk

Date: Wed, 21 Apr 2010 10:41:25 -0400

Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations
From: jampa...@gmail.com
To: g...@hotmail.com


Dear Berk,

Thanks for the reply, based on the suggestions of Justin from 
Mailing list i have tried the simulation in the following way.

1.
 I have removed the "acc_grps" option
2.
 I have used "energygrp_excl" to avoid
 interaction between non frozen-frozen and frozen-frozen.


Still i have seen some velocity to the frozen atoms (i have printed 
velocities from trajectory) and drift in the energy.

3. I also 
switched of PBC and used "coulombtype = different options here"  In this case
 i observed that some of the water molecules try to escape from the 
system.



But i am not clear about center of mass motion. Should i allow 
to change center of mass with "comm_mode = No" option?

Could you please 
let me know if you want more details about this? I am still struggling 
with running this simulation.


Thanks for your kind help
Srinivas.

-- 
*
J. Srinivasa Rao 
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group


Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off: 215-895-1989
Mob:  704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx


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*

J. Srinivasa Rao 
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off: 215-895-1989

Mob:  704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
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Re: [gmx-users] The problems of controling one atom through modifygromacs sourse code

[Carsten Kutzner]

Hi Chuan,

you might want to take a look at gmx_ga2la.h. The function
ga2la_home provides the local atom number for a given global
atom number (or returns FALSE if the atom is not found on the local
processor).

Carsten


On Apr 21, 2010, at 4:40 PM, 聂雪川 wrote:

> Hi,gmx-users,
>Now I want to control the motion of a certain atom (due to special 
> needs).So I added some codes like "if(n==my_atom)xprime[n][d]   = 
> x[n][d]+...;"  in the functionstatic "void do_update_md()" of the file 
> "gromacs-4.0.7\src\mdlib\update.c".But when mpi run,The gromacs performs a 
> domain decomposition algorithm ,which assign  a certain amount of atoms to 
> each CPU(The atoms called local atoms).But the serial number "n" of local 
> atoms always start from 0.So the code "if(n==my_atom)" is futile.
>Now I come into consideration to differentiate "my_atom" by its name.But I 
> am not sure about whether there exist the atom name at the the process of 
> mdrun.Or Is there a more simple way to  achieve it.
>  
> {The functions be involved with domain decomposition algorithm are:
>  
>  
> /src/mdlib/domdec.c(7458) void dd_partition_system()  (called by do_md())
>  
> /src/mdlib/domdec.c(3365) static void get_cg_distribution()
>  
> /src/mdlib/domdec_network.c(187)void dd_scatter()
>  
> }
>   Thank your.
>   chuan
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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[gmx-users] Understanding template.c

[Chandan Choudhury]

Hi gmx users !!

I want to read the trajectory file (*.trr ), produced as a result of mdrun.
I came to know that a file template.c already exists to facilate my process.
I could compile and execute the template.c. Like
printf("Atom name: %s\n",*(top.atoms.atomname[n]));
printf("Atom charge: %f\n",top.atoms.atom[n].q);
produces the Atom Name and the corresponding partial charges. respectively.
I could also print the x, y, z coordinate for each frame present in the trr
file.

What am I  looking for is, how can I print the Atom number, Residue name,
residue number? I was unable to find it in the program template.c.

I would also like to know how do you prompt -s / -f / -n etc. option during
executing gmx commands?

Thanks for your cooperation.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] Understanding template.c

[Mark Abraham]

On 22/04/2010 7:11 PM, Chandan Choudhury wrote:

Hi gmx users !!

I want to read the trajectory file (*.trr ), produced as a result of
mdrun. I came to know that a file template.c already exists to facilate
my process. I could compile and execute the template.c. Like
printf("Atom name: %s\n",*(top.atoms.atomname[n]));
printf("Atom charge: %f\n",top.atoms.atom[n].q);
produces the Atom Name and the corresponding partial charges.
respectively. I could also print the x, y, z coordinate for each frame
present in the trr file.

What am I  looking for is, how can I print the Atom number, Residue


They're probably also in the same data structure above - called "top". 
Search for its definition, and if necessary for the code where it is 
instantiated and filled with data.



name, residue number? I was unable to find it in the program template.c.


Sure - it's a template. It doesn't relieve you of the need to search the 
codebase for actual information. :-)



I would also like to know how do you prompt -s / -f / -n etc. option
during executing gmx commands?


I'm not sure what you mean by "prompt". Pick a GROMACS tool that does 
something similar to what you want, use a debugger to step through it to 
see how the code works, then use that information to modify an existing 
tool, or create your own copying and pasting useful bits.


Mark
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Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

[jampani srinivas]

Dear Berk,

I have run it for 5ns, as you said for first  1ns i have not seen much drift
in the energy there after energy is slowly increasing in each step. Should i
run it again and send you the edr file? can you please let me know on which
version of gromacs you have run this file?

Thanks very much
Srinivas.

On Thu, Apr 22, 2010 at 3:25 AM, Berk Hess  wrote:

>  Hi,
>
> I quickly ran the tpr file you provided on bugzilla, but I don't see an
> enormous energy drift.
> What do you mean with "the energy explodes"?
>
> Berk
>
> --
> Date: Wed, 21 Apr 2010 11:18:53 -0400
> Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve
> simiulations
> From: jampa...@gmail.com
> To: gmx-users@gromacs.org
>
>
> Dear Berk,
>
> I am sorry for poor communication, Herewith i am giving my md.mdp file. I
> this file as you could see i am using two temp coupling groups Tmp1 is
> protein and a 2nm spherical layer of water around it, and the second one
> Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K to it.
> As you could see that from the file below i have taken Tcoupl  =
> V-rescale and two coupling groups Tmp1 and Tmp2 to make a frozen wall. I am
> not accelerating any group here.
>
> In other words the goal of simulation is to check the behavior of protein
> is a confined sphere, i am trying to make frozen wall by freezing water
> around the protein after a specified distance.
>
>
> 
> title   = SS2130
> cpp = /usr/bin/cpp
> constraints = all-bonds
> integrator  = md
> dt  = 0.002 ; ps !
> nsteps  = 100
> nstxout = 1000
> nstvout = 1000
> nstfout = 0
> nstlog  = 0
> nstenergy   = 1000
> nstlist = 5
> ns_type = grid
> rlist   = 1.0
> coulombtype = PME
> rcoulomb= 1.0
> rvdw= 1.0
> rvdw_switch = 0.9
> fourierspacing  = 0.12
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> pme_order   = 4
> ewald_rtol  = 1e-5
> optimize_fft= yes
> Tcoupl  = V-rescale
> tau_t   = 0.1  0.1
> tc-grps = Tmp1 Tmp2
> ref_t   = 283.00.0
> gen_vel = yes
> gen_temp= 283.0
> gen_seed= 181726
> freezegrps  = Tmp2
> freezedim   = Y Y Y
> 
>
>
> Thanks very much
> Srinivas.
> On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess  wrote:
>
>  Hi,
>
> I moved this to the user list, so it will be of use to others.
>
> I have no clue what you are trying to do, what groups you are accelerating
> or freezing.
> So we can't help you without further information.
> Setting up simulations with frozen groups, accelerate groups or different
> coupling
> temperatures is tricky and will in most cases destroy energy conservation.
>
> Berk
>
> --
> Date: Wed, 21 Apr 2010 10:41:25 -0400
> Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations
> From: jampa...@gmail.com
> To: g...@hotmail.com
>
>
> Dear Berk,
>
> Thanks for the reply, based on the suggestions of Justin from Mailing list
> i have tried the simulation in the following way.
>
> 1. I have removed the "acc_grps" option
> 2. I have used "energygrp_excl" to avoid interaction between non
> frozen-frozen and frozen-frozen.
>
> Still i have seen some velocity to the frozen atoms (i have printed
> velocities from trajectory) and drift in the energy.
>
> 3. I also switched of PBC and used "coulombtype = different options here"
> In this case i observed that some of the water molecules try to escape from
> the system.
>
>
> But i am not clear about center of mass motion. Should i allow to change
> center of mass with "comm_mode = No" option?
>
> Could you please let me know if you want more details about this? I am
> still struggling with running this simulation.
>
> Thanks for your kind help
> Srinivas.
>
>
> --
> *
> J. Srinivasa Rao
> Post-doctoral Research Associate
> C/o Prof. Luis R Cruz Cruz
> Computational Biophysics Group
> Department of Physics
> Drexel University
> 3141 Chestnut St
> Philadelphia, PA 19104, USA.
> Ph:  Off: 215-895-1989
>Mob:  704-706-4191
> Web:http://jsrao.web.officelive.com/default.aspx
> **
>
>
>
> --
> New Windows 7: Find the right PC for you. Learn 
> more.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>
>
> --
> *
> J. Srinivasa Rao
> P

[gmx-users] the error for 2D periodic boundary

[kecy_wu]

 Hello,  when I use the 2D periodic boundary for the pr run , it just 
ran several steps then exited,  the log file has some error message like 
this :
Program mdrun, VERSION 4.0.5
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -1. It should have been within [ 0 .. 432 ]
If I use the 3D periodic boundary, it would be OK, but I have to use the 2D 
periodic boundary for my simulation, I don't know what is the reason. my 
pr.mdp file is below:
title  
 =  10tbppr
cpp
 =  /usr/bin/cpp 
define 
 =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt 
 =  0.002 ; ps !
nsteps 
 =  3 ; total 60.0 ps.
nstcomm 
=  1
nstxout 
=  100
nstvout 
=  100
nstfout 
=  0
nstlog 
 =  10
nstenergy   =  10
nstlist 
=  5 
ns_type 
=  grid
rlist  
 =  1.0 
; Eledtrostatics
coulombtype =  PME
rcoulomb    
=  1.0 ;distance for the coulomb cut-off
; VdW
vdwtype 
=  cut-off
rvdw   
 =  1.4 
DispCorr    = 
EnerPres
;Ewald
fourierspacing  =  0.3
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol  =  1e-5
ewald_geometry  =  
3dc    
optimize_fft  =  yes
;Pbc and walls
pbc
 =  xy  ;ns_type must be grid
nwall  
 =  2
wall_type  
 =  10-4
wall_atomtype   = SI 
SI
wall_density    
= 10 10
wall_r_linpot   
=  0.5
; Berendsen temperature coupling is on in three groups
Tcoupl 
 =  v-rescale
tau_t  
 =  0.1 0.1 0.1
tc_grps  = SOL C12 TBP
ref_t  
 =  300 300 300
; Pressure coupling is on
Pcoupl 
 =  parrinello-rahman 
pcoupltype  =  
semiisotropic
tau_p  
 =  0.5
compressibility =  0 4.5e-5
ref_p  
 =  1.0 1.0
; Generate velocites is on at 300 K.
gen_vel 
=  yes
gen_temp    
=  300.0
gen_seed    
=  -1
 could  you help me analyze the reason? thank you very much !-- 
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[gmx-users] .mtx file

[Nilesh Dhumal]

Hello,
I am trying to calculate the normal mode analysis for ionic liquids.
I could do energy minimzation. I could not get .mtx file for further
analysis to get normal modes.

THis is my energy minimization file

define   = -DFLEXIBLE

constraints  = none

integrator   = L-bfgs

tinit= 0

nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency

nstlist  = 0

; ns algorithm (simple or grid)

ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc  = no

; nblist cut-off

rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics
coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field

epsilon-r= 1

; Method for doing Van der Waals

vdw-type = Cut-off

; cut-off lengths

rvdw-switch  = 0

rvdw = 0


grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top

 mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx

I could not get the new_nm.mtx file.
Can you tell me where I am going wrong.

THanks

Nilesh



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Re: [gmx-users] .mtx file

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,
I am trying to calculate the normal mode analysis for ionic liquids.
I could do energy minimzation. I could not get .mtx file for further
analysis to get normal modes.

THis is my energy minimization file

define   = -DFLEXIBLE

constraints  = none

integrator   = L-bfgs

tinit= 0

nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency

nstlist  = 0

; ns algorithm (simple or grid)

ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc  = no

; nblist cut-off

rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics
coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field

epsilon-r= 1

; Method for doing Van der Waals

vdw-type = Cut-off

; cut-off lengths

rvdw-switch  = 0

rvdw = 0


grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top



Be careful about setting -zero.  If you're trying to get past error messages, 
that usually means you have missing parameters and could end up with nonsense as 
a result.



 mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx

I could not get the new_nm.mtx file.
Can you tell me where I am going wrong.



You aren't getting the .mtx file because you're telling mdrun to do energy 
minimization, not normal modes.  L-BFGS is an EM method.  Set "integrator = nm" 
to do normal modes.


-Justin


THanks

Nilesh





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] make_edi

[vijaya subramanian]

Hi
When I run make_edi with a small eigenvec.trr file it works, but gives me a 
segmentation fault when I input large .trr files generated using g_covar.  
These large eigenvector
files work well with g_anaeig and I have used them to generate projections as 
well as filtered trajectories.
The command line with options for make_edi is given below: 

make_edi -linfix "4,5,7,8" -outfrq 500 -f eigvec.trr -s fframe.gro  -o 
edsamp.edi -linstep ".0001 .0001 .0001 .0001"


One option would be to read the large eigenvec.trr file and write out only the 
eigenvectors
I need to a new file.  Is there some way I can do that?  Else, is there some 
way to modify
make_edi so I don't get a segmentation fault.

Thanks
Vijaya
  
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[gmx-users] Magic error xtc?

[nishap . patel]

Hello,

I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)


Checking file md.part0002.xtc
Reading frame   0 time 48190.004
# Atoms  6533
Precision 0.001 (nm)
Reading frame  178000 time 83790.008

Part one of the simulation ran fine, but it exceeded the run time so I  
ran it again, and got part0002.xtc file. Now it seems like my  
part0002.xtc file is corrupted, is there a way I can just run my  
simulation again from my first file without running the whole thing  
again?


Thanks.


N.P


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Re: [gmx-users] Magic error xtc?

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:

Hello,

I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)


Checking file md.part0002.xtc
Reading frame   0 time 48190.004
# Atoms  6533
Precision 0.001 (nm)
Reading frame  178000 time 83790.008

Part one of the simulation ran fine, but it exceeded the run time so I 
ran it again, and got part0002.xtc file. Now it seems like my 
part0002.xtc file is corrupted, is there a way I can just run my 
simulation again from my first file without running the whole thing again?




That's the nice part about checkpointing.  As long as you have the .cpt file 
from wherever you started the continuation, you can just re-run from that same 
point.  That's really what you did in the first place.  If, for some reason, 
you've over-written or deleted that .cpt file, then you can only start from some 
later .cpt file, or in the worst case, all over again.


-Justin


Thanks.


N.P




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Magic error xtc?

[nishap . patel]

Hi Justin,

Well the way I continued my second part of the simulation was  
using my md.cpt file. I checked my .cpt file and this is what I got:
Last frame -1 time 83786.961 , so I guess my second run  
updated the file, so does this mean I have to do the whole simulation  
again? or can I use any of the other files for example .trr file? I  
thought it might be that I don't have enough disk space?





Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

   I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)


Checking file md.part0002.xtc
Reading frame   0 time 48190.004
# Atoms  6533
Precision 0.001 (nm)
Reading frame  178000 time 83790.008

Part one of the simulation ran fine, but it exceeded the run time   
so I ran it again, and got part0002.xtc file. Now it seems like my   
part0002.xtc file is corrupted, is there a way I can just run my   
simulation again from my first file without running the whole thing  
 again?




That's the nice part about checkpointing.  As long as you have the .cpt
file from wherever you started the continuation, you can just re-run
from that same point.  That's really what you did in the first place.
If, for some reason, you've over-written or deleted that .cpt file,
then you can only start from some later .cpt file, or in the worst
case, all over again.

-Justin


Thanks.


N.P




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Magic error xtc?

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:

Hi Justin,

Well the way I continued my second part of the simulation was using 
my md.cpt file. I checked my .cpt file and this is what I got:
Last frame -1 time 83786.961 , so I guess my second run updated 
the file, so does this mean I have to do the whole simulation again? or 
can I use any of the other files for example .trr file? I thought it 
might be that I don't have enough disk space?




Checkpoint files will over-write each other, but a backup is kept as 
(whatever)_prev.cpt; you may be able to use this file to re-start your run.  If 
md.cpt corresponds to a time where there is a viable frame in your trajectory, 
then there should be no problem re-starting it from this .cpt file.  That is, if 
the frame at (or after) 83790 is corrupt, re-starting from time 83786 should 
present no problem.


Maybe you're out of disk space, but only you know if that's the problem :)

-Justin





Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

   I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)


Checking file md.part0002.xtc
Reading frame   0 time 48190.004
# Atoms  6533
Precision 0.001 (nm)
Reading frame  178000 time 83790.008

Part one of the simulation ran fine, but it exceeded the run time  so 
I ran it again, and got part0002.xtc file. Now it seems like my  
part0002.xtc file is corrupted, is there a way I can just run my  
simulation again from my first file without running the whole thing 
 again?




That's the nice part about checkpointing.  As long as you have the .cpt
file from wherever you started the continuation, you can just re-run
from that same point.  That's really what you did in the first place.
If, for some reason, you've over-written or deleted that .cpt file,
then you can only start from some later .cpt file, or in the worst
case, all over again.

-Justin


Thanks.


N.P




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] make_edi, more info

[vijaya subramanian]

 Hi
I have included the output from two make_edi submissions, the first one gave
a segmentation fault and the second did not.  The only difference between the 
two is the input .trr file.  
:-)  make_edi  (-:

Option Filename  Type Description

  -f evec11-129.trr  InputFull precision trajectory: trr trj cpt
-eig   eigenval.xvg  Input, Opt.  xvgr/xmgr file
  -s fframe4-1250ps.gro  InputStructure+mass(db): tpr tpb tpa gro g96
   pdb
  -n  index.ndx  Input, Opt.  Index file
-tar target.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
-ori origin.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -o edsamp.edi  Output   ED sampling input

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-mon string Indices of eigenvectors for projections of x
(e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91
-linfix  string 4,5,7,8  Indices of eigenvectors for fixed increment
linear sampling
-linacc  string Indices of eigenvectors for acceptance linear
sampling
-flood   string Indices of eigenvectors for flooding
-radfix  string Indices of eigenvectors for fixed increment
radius expansion
-radacc  string Indices of eigenvectors for acceptance radius
expansion
-radcon  string Indices of eigenvectors for acceptance radius
contraction
-outfrq  int5000Freqency (in steps) of writing output in .edo file
-slope   real   0   Minimal slope in acceptance radius expansion
-maxedsteps  int0   Max nr of steps per cycle
-deltaF0 real   150 Target destabilization energy  - used for flooding
-deltaF  real   0   Start deltaF with this parameter - default 0,
i.e. nonzero values only needed for restart
-tau real   0.1 Coupling constant for adaption of flooding
strength according to deltaF0, 0 = infinity i.e.
constant flooding strength
-eqsteps int0   Number of steps to run without any perturbations 
-Eflnull real   0   This is the starting value of the flooding
strength. The flooding strength is updated
according to the adaptive flooding scheme. To use
a constant flooding strength use -tau 0. 
-T   real   300 T is temperature, the value is needed if you want
to do flooding 
-alpha   real   1   Scale width of gaussian flooding potential with
alpha^2 
-linstep string .0001 .0001 .0001 .0001  Stepsizes (nm/step) for fixed
increment linear sampling (put in quotes! "1.0
2.3 5.1 -3.1")
-accdir  string Directions for acceptance linear sampling - only
sign counts! (put in quotes! "-1 +1 -1.1")
-radstep real   0   Stepsize (nm/step) for fixed increment radius
expansion
-[no]restrain  bool no  Use the flooding potential with inverted sign ->
effects as quasiharmonic restraining potential
-[no]hessian bool   no  The eigenvectors and eigenvalues are from a
Hessian matrix
-[no]harmonic  bool no  The eigenvalues are interpreted as spring constant

list -linfix consist of the indices:4 5 7 8 
list -linacc consist of the indices:
list -flood consist of the indices:
list -radfix consist of the indices:
list -radacc consist of the indices:
list -radcon consist of the indices:
list -mon consist of the indices:
trn version: GMX_trn_file (single precision)
Eigenvectors in evec11-129.trr were determined without fitting
Read non mass weighted average/minimum structure with 4128 atoms from 
evec11-129.trr
Read 12384 eigenvectors (for 4128 atoms)


Select an index group of 4128 elements that corresponds to the eigenvectors
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has  4128 elements
Group 1 ( Protein) has  4128 elements
Group 2 (   Protein-H) has  4128 elements
Group 3 ( C-alpha) has  4128 elements
Group 4 (Backbone) has  4128 elements
Group 5 (   MainChain) has  4128 elements
Group 6 (MainChain+Cb) has  4128 elements
Group 7 ( MainChain+H) has  412

[gmx-users] No Temperature Coupling to protein

[Ricardo O. S. Soares]

Hi gmx users,

I'd like to run a test simulation, in which the temperature coupling is not 
on for the protein, yet active for the solvent and ions.  If I specify in the 
tc-grps only "Non-protein", the grompp complains (Fatal error) that there are 
some atoms (the ones of the protein) out of the coupling group. Is there a way 
to do that in gromacs? 
   
Thanks.

 


---
 Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.
Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
Phone: +55 16 36024840.

ross_...@yahoo.com.br,rsoa...@fcfrp.usp.br


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Re: [gmx-users] Magic error xtc?

[Tsjerk Wassenaar]

Hey,

Otherwise it's also still possible to do old style continuation with a
frame from the .trr/.edr file, provided you have those...

Cheers,

Tsjerk

On Thu, Apr 22, 2010 at 7:55 PM, Justin A. Lemkul  wrote:
>
>
> nishap.pa...@utoronto.ca wrote:
>>
>> Hi Justin,
>>
>>    Well the way I continued my second part of the simulation was using my
>> md.cpt file. I checked my .cpt file and this is what I got:
>> Last frame         -1 time 83786.961 , so I guess my second run updated
>> the file, so does this mean I have to do the whole simulation again? or can
>> I use any of the other files for example .trr file? I thought it might be
>> that I don't have enough disk space?
>>
>
> Checkpoint files will over-write each other, but a backup is kept as
> (whatever)_prev.cpt; you may be able to use this file to re-start your run.
>  If md.cpt corresponds to a time where there is a viable frame in your
> trajectory, then there should be no problem re-starting it from this .cpt
> file.  That is, if the frame at (or after) 83790 is corrupt, re-starting
> from time 83786 should present no problem.
>
> Maybe you're out of disk space, but only you know if that's the problem :)
>
> -Justin
>
>>
>>
>>
>> Quoting "Justin A. Lemkul" :
>>
>>>
>>>
>>> nishap.pa...@utoronto.ca wrote:

 Hello,

   I am running simulations and I got Magic Number error: Fatal error:
 Magic Number Error in XTC file (read 0, should be 1995)


 Checking file md.part0002.xtc
 Reading frame       0 time 48190.004
 # Atoms  6533
 Precision 0.001 (nm)
 Reading frame  178000 time 83790.008

 Part one of the simulation ran fine, but it exceeded the run time  so I
 ran it again, and got part0002.xtc file. Now it seems like my  part0002.xtc
 file is corrupted, is there a way I can just run my  simulation again from
 my first file without running the whole thing  again?

>>>
>>> That's the nice part about checkpointing.  As long as you have the .cpt
>>> file from wherever you started the continuation, you can just re-run
>>> from that same point.  That's really what you did in the first place.
>>> If, for some reason, you've over-written or deleted that .cpt file,
>>> then you can only start from some later .cpt file, or in the worst
>>> case, all over again.
>>>
>>> -Justin
>>>
 Thanks.


 N.P


>>>
>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> --
>>> gmx-users mailing list    gmx-us...@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>>
>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [gmx-users] No Temperature Coupling to protein

[Justin A. Lemkul]

Ricardo O. S. Soares wrote:

Hi gmx users,

I'd like to run a test simulation, in which the temperature coupling 
is not on for the protein, yet active for the solvent and ions.  If I 
specify in the tc-grps only "Non-protein", the grompp complains (Fatal 
error) that there are some atoms (the ones of the protein) out of the 
coupling group. Is there a way to do that in gromacs?


Per the manual, in the entry for tau_t: "time constant for coupling (one for 
each group in tc_grps), 0 means no temperature coupling"


Whether or not this has any physical significance will depend on your purpose, 
but as long as all the atoms are actually accounted for, Gromacs will let you 
play around with the thermostats pretty flexibly :)


-Justin

  
Thanks.
 




---

 


Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São 
Paulo.

Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
Phone: +55 16 36024840.


ross_...@yahoo.com.br,rsoa...@fcfrp.usp.br

 





 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Magic error xtc?

[nishap . patel]

I am trying using prev_md.cpt file. I checked and it looks okay, so  
hopefully it will work. If not I will try using .trr files.

Thanks



Quoting Tsjerk Wassenaar :


Hey,

Otherwise it's also still possible to do old style continuation with a
frame from the .trr/.edr file, provided you have those...

Cheers,

Tsjerk

On Thu, Apr 22, 2010 at 7:55 PM, Justin A. Lemkul  wrote:



nishap.pa...@utoronto.ca wrote:


Hi Justin,

   Well the way I continued my second part of the simulation was using my
md.cpt file. I checked my .cpt file and this is what I got:
Last frame         -1 time 83786.961 , so I guess my second run updated
the file, so does this mean I have to do the whole simulation again? or can
I use any of the other files for example .trr file? I thought it might be
that I don't have enough disk space?



Checkpoint files will over-write each other, but a backup is kept as
(whatever)_prev.cpt; you may be able to use this file to re-start your run.
 If md.cpt corresponds to a time where there is a viable frame in your
trajectory, then there should be no problem re-starting it from this .cpt
file.  That is, if the frame at (or after) 83790 is corrupt, re-starting
from time 83786 should present no problem.

Maybe you're out of disk space, but only you know if that's the problem :)

-Justin





Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:


Hello,

  I am running simulations and I got Magic Number error: Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)


Checking file md.part0002.xtc
Reading frame       0 time 48190.004
# Atoms  6533
Precision 0.001 (nm)
Reading frame  178000 time 83790.008

Part one of the simulation ran fine, but it exceeded the run time  so I
ran it again, and got part0002.xtc file. Now it seems like my   
 part0002.xtc
file is corrupted, is there a way I can just run my  simulation   
again from

my first file without running the whole thing  again?



That's the nice part about checkpointing.  As long as you have the .cpt
file from wherever you started the continuation, you can just re-run
from that same point.  That's really what you did in the first place.
If, for some reason, you've over-written or deleted that .cpt file,
then you can only start from some later .cpt file, or in the worst
case, all over again.

-Justin


Thanks.


N.P




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Can't post? Read http://www.gromacs.org/mailing_lists/users.php









--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
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Re: [gmx-users] .mtx file

[Nilesh Dhumal]

Hello Justin,
I could genrate the .mtx file. I followed following steps.

 g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr

 g_nmtraj -s 1.tpr -v test1.trr -o test.xtc

 g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg

and

g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -s 1.tpr -o ensemble.xtc

For last analysis (g_nmens) I get following error.

Fatal error:Sorry, write_trxframe_indexed can not write tpa

Can you help me resolve this error.

NIlesh


On Thu, April 22, 2010 12:55 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>> I am trying to calculate the normal mode analysis for ionic liquids.
>> I could do energy minimzation. I could not get .mtx file for further
>> analysis to get normal modes.
>>
>> THis is my energy minimization file
>>
>>
>> define   = -DFLEXIBLE
>>
>> constraints  = none
>>
>> integrator   = L-bfgs
>>
>> tinit= 0
>>
>> nsteps   = 15000
>>
>> nbfgscorr= 50
>>
>> emtol= .001
>>
>> emstep   = 0.1
>>
>> gen_vel  = yes
>>
>> gen-temp = 300
>>
>> nstcomm  =  1
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>>
>>
>> nstlist  = 0
>>
>> ; ns algorithm (simple or grid)
>>
>>
>> ns-type  = simple
>>
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>>
>>
>> ; or full (infinite systems only)
>>
>>
>> pbc  = no
>>
>> ; nblist cut-off
>>
>>
>> rlist= 0
>>
>> domain-decomposition = no
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>
>>
>> ; Method for doing electrostatics
>> coulombtype  = Cut-Off
>>
>> rcoulomb-switch  = 0
>>
>> rcoulomb = 0
>>
>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>>
>>
>> epsilon-r= 1
>>
>> ; Method for doing Van der Waals
>>
>>
>> vdw-type = Cut-off
>>
>> ; cut-off lengths
>>
>>
>> rvdw-switch  = 0
>>
>> rvdw = 0
>>
>>
>> grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top
>>
>
> Be careful about setting -zero.  If you're trying to get past error
> messages, that usually means you have missing parameters and could end up
> with nonsense as a result.
>
>> mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx
>>
>> I could not get the new_nm.mtx file.
>> Can you tell me where I am going wrong.
>>
>>
>
> You aren't getting the .mtx file because you're telling mdrun to do
> energy minimization, not normal modes.  L-BFGS is an EM method.  Set
> "integrator = nm"
> to do normal modes.
>
> -Justin
>
>
>> THanks
>>
>>
>> Nilesh
>>
>>
>>
>>
>
> --
> 
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>


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Re: [gmx-users] .mtx file

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello Justin,
I could genrate the .mtx file. I followed following steps.

 g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr

 g_nmtraj -s 1.tpr -v test1.trr -o test.xtc

 g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg

and

g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -s 1.tpr -o ensemble.xtc

For last analysis (g_nmens) I get following error.

Fatal error:Sorry, write_trxframe_indexed can not write tpa

Can you help me resolve this error.


Did the above g_nmens command come directly from a copy-paste from your 
terminal?  Looking into the code, I see no way that writing an .xtc file would 
be misinterpreted as writing a binary topology, thus giving that error.  Check 
for typos, specifically in the file extension.  If you're using the default 
output file name, you don't even have to specify it.


If it still doesn't work, report back.  It might also be useful to know your 
Gromacs version in case of problems.


-Justin



NIlesh


On Thu, April 22, 2010 12:55 pm, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Hello,
I am trying to calculate the normal mode analysis for ionic liquids.
I could do energy minimzation. I could not get .mtx file for further
analysis to get normal modes.

THis is my energy minimization file


define   = -DFLEXIBLE

constraints  = none

integrator   = L-bfgs

tinit= 0

nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency


nstlist  = 0

; ns algorithm (simple or grid)


ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)


; or full (infinite systems only)


pbc  = no

; nblist cut-off


rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW


; Method for doing electrostatics
coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


epsilon-r= 1

; Method for doing Van der Waals


vdw-type = Cut-off

; cut-off lengths


rvdw-switch  = 0

rvdw = 0


grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top


Be careful about setting -zero.  If you're trying to get past error
messages, that usually means you have missing parameters and could end up
with nonsense as a result.


mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx

I could not get the new_nm.mtx file.
Can you tell me where I am going wrong.



You aren't getting the .mtx file because you're telling mdrun to do
energy minimization, not normal modes.  L-BFGS is an EM method.  Set
"integrator = nm"
to do normal modes.

-Justin



THanks


Nilesh





--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 don't post (un)subscribe requests to the list. Use the
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http://www.gromacs.org/mailing_lists/users.php









--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] .mtx file

[Nilesh Dhumal]

Hello Justin

In manual (Manual-4.0) and  g_nmens -h (help), the extension of output
file is .xtc. If I use the default output file name still I am getting the
same error.

Nilesh

On Thu, April 22, 2010 4:01 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello Justin,
>> I could genrate the .mtx file. I followed following steps.
>>
>>
>> g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr
>>
>> g_nmtraj -s 1.tpr -v test1.trr -o test.xtc
>>
>> g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg
>>
>> and
>>
>> g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -s 1.tpr -o
>> ensemble.xtc
>>
>> For last analysis (g_nmens) I get following error.
>>
>>
>> Fatal error:Sorry, write_trxframe_indexed can not write tpa
>>
>>
>> Can you help me resolve this error.
>>
>
> Did the above g_nmens command come directly from a copy-paste from your
> terminal?  Looking into the code, I see no way that writing an .xtc file
> would be misinterpreted as writing a binary topology, thus giving that
> error.  Check for typos, specifically in the file extension.  If you're
> using the default output file name, you don't even have to specify it.
>
> If it still doesn't work, report back.  It might also be useful to know
> your Gromacs version in case of problems.
>
>
> -Justin
>
>
>>
>> NIlesh
>>
>>
>>
>> On Thu, April 22, 2010 12:55 pm, Justin A. Lemkul wrote:
>>
>>
>>> Nilesh Dhumal wrote:
>>>
>>>
 Hello,
 I am trying to calculate the normal mode analysis for ionic liquids.
  I could do energy minimzation. I could not get .mtx file for
 further analysis to get normal modes.

 THis is my energy minimization file



 define   = -DFLEXIBLE

 constraints  = none

 integrator   = L-bfgs

 tinit= 0

 nsteps   = 15000

 nbfgscorr= 50

 emtol= .001

 emstep   = 0.1

 gen_vel  = yes

 gen-temp = 300

 nstcomm  =  1

 ; NEIGHBORSEARCHING PARAMETERS
 ; nblist update frequency



 nstlist  = 0

 ; ns algorithm (simple or grid)



 ns-type  = simple

 ; Periodic boundary conditions: xyz (default), no (vacuum)



 ; or full (infinite systems only)



 pbc  = no

 ; nblist cut-off



 rlist= 0

 domain-decomposition = no

 ; OPTIONS FOR ELECTROSTATICS AND VDW



 ; Method for doing electrostatics
 coulombtype  = Cut-Off

 rcoulomb-switch  = 0

 rcoulomb = 0

 ; Dielectric constant (DC) for cut-off or DC of reaction field



 epsilon-r= 1

 ; Method for doing Van der Waals



 vdw-type = Cut-off

 ; cut-off lengths



 rvdw-switch  = 0

 rvdw = 0


 grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top


>>> Be careful about setting -zero.  If you're trying to get past error
>>> messages, that usually means you have missing parameters and could end
>>> up with nonsense as a result.
>>>
 mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx

 I could not get the new_nm.mtx file.
 Can you tell me where I am going wrong.



>>> You aren't getting the .mtx file because you're telling mdrun to do
>>> energy minimization, not normal modes.  L-BFGS is an EM method.  Set
>>> "integrator = nm"
>>> to do normal modes.
>>>
>>> -Justin
>>>
>>>
>>>
 THanks



 Nilesh





>>> --
>>> 
>>>
>>>
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> 
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/P

Re: [gmx-users] .mtx file

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello Justin

In manual (Manual-4.0) and  g_nmens -h (help), the extension of output
file is .xtc. If I use the default output file name still I am getting the
same error.



I know what the help information says, I was just trying to clarify if what you 
had shown was actually a direct copy-and-paste from a terminal or something else 
processed through your memory.  Whether or not you were specifying the same 
output name as default (or thought you were) is irrelevant, I was just 
suggesting a test - don't specify anything at all for the -o flag, just in case 
you made some sort of typo.  If you get the same error when you are not 
specifying anything at all with -o, then at least post the Gromacs version 
you're using (which I asked for before) to see if any of the developers has an 
idea about what could be going on.  If the default output is giving a fatal 
error, something is probably wrong in the code.


-Justin


Nilesh

On Thu, April 22, 2010 4:01 pm, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Hello Justin,
I could genrate the .mtx file. I followed following steps.


g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr

g_nmtraj -s 1.tpr -v test1.trr -o test.xtc

g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg

and

g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -s 1.tpr -o
ensemble.xtc

For last analysis (g_nmens) I get following error.


Fatal error:Sorry, write_trxframe_indexed can not write tpa


Can you help me resolve this error.


Did the above g_nmens command come directly from a copy-paste from your
terminal?  Looking into the code, I see no way that writing an .xtc file
would be misinterpreted as writing a binary topology, thus giving that
error.  Check for typos, specifically in the file extension.  If you're
using the default output file name, you don't even have to specify it.

If it still doesn't work, report back.  It might also be useful to know
your Gromacs version in case of problems.


-Justin



NIlesh



On Thu, April 22, 2010 12:55 pm, Justin A. Lemkul wrote:



Nilesh Dhumal wrote:



Hello,
I am trying to calculate the normal mode analysis for ionic liquids.
 I could do energy minimzation. I could not get .mtx file for
further analysis to get normal modes.

THis is my energy minimization file



define   = -DFLEXIBLE

constraints  = none

integrator   = L-bfgs

tinit= 0

nsteps   = 15000

nbfgscorr= 50

emtol= .001

emstep   = 0.1

gen_vel  = yes

gen-temp = 300

nstcomm  =  1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency



nstlist  = 0

; ns algorithm (simple or grid)



ns-type  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)



; or full (infinite systems only)



pbc  = no

; nblist cut-off



rlist= 0

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW



; Method for doing electrostatics
coulombtype  = Cut-Off

rcoulomb-switch  = 0

rcoulomb = 0

; Dielectric constant (DC) for cut-off or DC of reaction field



epsilon-r= 1

; Method for doing Van der Waals



vdw-type = Cut-off

; cut-off lengths



rvdw-switch  = 0

rvdw = 0


grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top



Be careful about setting -zero.  If you're trying to get past error
messages, that usually means you have missing parameters and could end
up with nonsense as a result.


mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx

I could not get the new_nm.mtx file.
Can you tell me where I am going wrong.




You aren't getting the .mtx file because you're telling mdrun to do
energy minimization, not normal modes.  L-BFGS is an EM method.  Set
"integrator = nm"
to do normal modes.

-Justin




THanks



Nilesh






--




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php








--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages

[gmx-users] Re: No Temperature Coupling to protein (Justin A. Lemkul)

[Ricardo O. S. Soares]

Oh yes I see, thanks Justin!


Ricardo O. S. Soares wrote:
> Hi gmx users,
> 
> I'd like to run a test simulation, in which the temperature coupling 
> is not on for the protein, yet active for the solvent and ions.  If I 
> specify in the tc-grps only "Non-protein", the grompp complains (Fatal 
> error) that there are some atoms (the ones of the protein) out of the 
> coupling group. Is there a way to do that in gromacs?

Per the manual, in the entry for tau_t: "time constant for coupling (one for 
each group in tc_grps), 0 means no temperature coupling"

Whether or not this has any physical significance will depend on your purpose, 
but as long as all the atoms are actually accounted for, Gromacs will let you 
play around with the thermostats pretty flexibly :)

-Justin

>  
> Thanks.
 


---
 Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.
Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
Phone: +55 16 36024840.

ross_...@yahoo.com.br,rsoa...@fcfrp.usp.br


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[gmx-users] grompp, energy minimization,, output file error

[Moeed]

Dear gmx users,

I am trying to run grompp program to preprocess the input files. input gro
file contains coordinates of a stack of hexane molecules (256 molecules).

grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em -maxwarn
30 >& output.grompp_em


my problem is that output: Hexane_em.tpr contains strange notations:

é...@!`a‰7kÇ?ý"Ðå`a...@!(r° Äœ@(LÍ?û i�...@!o\(õ @(LÍ?ù n— o...@!
¾vÈ´9@(lÍ?öí‘hr...@!f§ï
²-@(lÍ?ôýó¶e�...@!


output.grompp_em:


  GNU nano 2.0.9File:
output.grompp_em


Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HEX'

NOTE 1 [file HexaneModified.top, line 163]:
  System has non-zero total charge: 2.206157e+04



processing coordinates...

Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C1)
Warning: atom name 2 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C2)
Warning: atom name 3 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C3)
Warning: atom name 4 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C4)
Warning: atom name 5 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C5)
Warning: atom name 6 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C6)
Warning: atom name 7 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H1)
Warning: atom name 8 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H2)
Warning: atom name 9 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H3)
Warning: atom name 10 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H4)
Warning: atom name 11 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H5)
Warning: atom name 12 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H6)
Warning: atom name 13 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H7)
Warning: atom name 14 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H8)
Warning: atom name 15 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H9)
Warning: atom name 16 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H10)
Warning: atom name 17 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H11)

WARNING 1 [file HexaneModified.top, line 163]:
  5120 non-matching atom names
  atom names from HexaneModified.top will be used
  atom names from Hexane-stack.gro will be ignored


double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

NOTE 2 [file HexaneModified.top, line unknown]:
  The largest charge group contains 20 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat

Making dummy/rest group for T-Coupling containing 5120 elements
Making dummy/rest group for Acceleration containing 5120 elements
Making dummy/rest group for Freeze containing 5120 elements
Making dummy/rest group for Energy Mon. containing 5120 elements
Making dummy/rest group for VCM containing 5120 elements
Number of degrees of freedom in T-Coupling group rest is 15357.00
Making dummy/rest group for User1 containing 5120 elements
Making dummy/rest group for User2 containing 5120 elements
Making dummy/rest group for XTC containing 5120 elements
Making dummy/rest group for Or. Res. Fit containing 5120 elements
Making dummy/rest group for QMMM containing 5120 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest

Checking consistency between energy and charge groups...

NOTE 3 [file em.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


writing run input file...

There were 3 notes

There was 1 warning

Back Off! I just backed up Hexane_em.tpr to ./#Hexane_em.tpr.1#

gcq#312: "Move about like a Scientist, lay down, get kissed" (Red Hot Chili
Peppars)


processing topology...
Analysing residue names:
There are:   256  OTHER residues
There are: 0PROTEIN residues
There are: 0DNA residues
Analysing Other...
This run will 

Re: [gmx-users] grompp, energy minimization,, output file error

[Mark Abraham]

On 23/04/2010 8:52 AM, Moeed wrote:

Dear gmx users,

I am trying to run grompp program to preprocess the input files. input
gro file contains coordinates of a stack of hexane molecules (256
molecules).

grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em
-maxwarn 30 >& output.grompp_em


Don't use -maxwarn unless you know why the warnings may be ignored.


my problem is that output: Hexane_em.tpr contains strange notations:

é...@!`a‰7kÇ?ý"Ðå`a...@!(r° Äœ@(LÍ?û i�...@!o\(õ @(LÍ?ù n— o...@!
¾vÈ´9@(lÍ?öí‘hr...@!f§ï ²-@(lÍ?ôýó¶e�...@!


It's a binary file. Don't try to read it with a text reader. GROMACS 
provides the gmxdump utility to get at the information, but that won't 
help you here.



output.grompp_em:


   GNU nano 2.0.9File: output.grompp_em


Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HEX'

NOTE 1 [file HexaneModified.top, line 163]:
   System has non-zero total charge: 2.206157e+04


Your system has a charge of 22061.57. This is because you've broken your 
[atoms] section. See below.



processing coordinates...

Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C1)


Another symptom of the above.


Warning: atom name 2 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C2)
Warning: atom name 3 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C3)
Warning: atom name 4 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C4)
Warning: atom name 5 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C5)
Warning: atom name 6 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C6)
Warning: atom name 7 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H1)
Warning: atom name 8 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H2)
Warning: atom name 9 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H3)
Warning: atom name 10 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H4)
Warning: atom name 11 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H5)
Warning: atom name 12 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H6)
Warning: atom name 13 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H7)
Warning: atom name 14 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H8)
Warning: atom name 15 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H9)
Warning: atom name 16 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H10)
Warning: atom name 17 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H11)

WARNING 1 [file HexaneModified.top, line 163]:
   5120 non-matching atom names
   atom names from HexaneModified.top will be used
   atom names from Hexane-stack.gro will be ignored


double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

NOTE 2 [file HexaneModified.top, line unknown]:
   The largest charge group contains 20 atoms.
   Since atoms only see each other when the centers of geometry of the
charge
   groups they belong to are within the cut-off distance, too large charge
   groups can lead to serious cut-off artifacts.
   For efficiency and accuracy, charge group should consist of a few atoms.
   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Another symptom.


initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat

Making dummy/rest group for T-Coupling containing 5120 elements
Making dummy/rest group for Acceleration containing 5120 elements
Making dummy/rest group for Freeze containing 5120 elements
Making dummy/rest group for Energy Mon. containing 5120 elements
Making dummy/rest group for VCM containing 5120 elements
Number of degrees of freedom in T-Coupling group rest is 15357.00
Making dummy/rest group for User1 containing 5120 elements
Making dummy/rest group for User2 containing 5120 elements
Making dummy/rest group for XTC containing 5120 elements
Making dummy/rest group for Or. Res. Fit containing 5120 elements
Making dummy/rest group for QMMM containing 5120 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest

Checking consistency between energy and charge groups...

NOTE 3 [file em.mdp, line unknown]:
   You are using a plain Coulomb cut-off, which might produce artifacts.
   You might want to consider u

Re: [gmx-users] grompp, energy minimization,, output file error

[Justin A. Lemkul]

Moeed wrote:

Dear gmx users,

I am trying to run grompp program to preprocess the input files. input 
gro file contains coordinates of a stack of hexane molecules (256 
molecules).


grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em 
-maxwarn 30 >& output.grompp_em



my problem is that output: Hexane_em.tpr contains strange notations:

é...@!`a‰7kÇ?ý"Ðå`a...@!(r° Äœ@(LÌÌÌÌÍ?û iÂ...@!o\(õ @(LÌÌÌÌÍ?ù n— o...@! 
¾vÈ´9@(lÌÌÌÌÍ?öí‘hr...@!f§ï ²-@(lÌÌÌÌÍ?ôýó¶eÂ...@!





A .tpr file is binary.  You won't be able to read it.


output.grompp_em:


  GNU nano 2.0.9File: 
output.grompp_em   



Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HEX'

NOTE 1 [file HexaneModified.top, line 163]:
  System has non-zero total charge: 2.206157e+04



This line is very concerning.  You have a net charge in excess of +22000! 
Something is badly broken in your topology.





processing coordinates...

Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not 
match (1 - C1)


These errors all indicate that you either have something out of order in your 
[molecules] directive (it has to match the order of the molecules in the 
coordinate file) or you have an improperly-formatted coordinate file.






NOTE 2 [file HexaneModified.top, line unknown]:
  The largest charge group contains 20 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.



See the manual for the group concept.  Large charge groups can cause bad 
electrostatics artifacts.



initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat

Making dummy/rest group for T-Coupling containing 5120 elements
Making dummy/rest group for Acceleration containing 5120 elements
Making dummy/rest group for Freeze containing 5120 elements
Making dummy/rest group for Energy Mon. containing 5120 elements
Making dummy/rest group for VCM containing 5120 elements
Number of degrees of freedom in T-Coupling group rest is 15357.00
Making dummy/rest group for User1 containing 5120 elements
Making dummy/rest group for User2 containing 5120 elements
Making dummy/rest group for XTC containing 5120 elements
Making dummy/rest group for Or. Res. Fit containing 5120 elements
Making dummy/rest group for QMMM containing 5120 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest

Checking consistency between energy and charge groups...

NOTE 3 [file em.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.



There is also very little justification for using plain cutoffs.  Heed the 
warning and use a more reasonable (and modern) setting.





[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1   opls_157  1C1  1  -0.18 12.011   ; 
qtot -0.18
 2   opls_158  1C2  1  -0.12 12.011   ; 
qtot -0.3
 3   opls_158  1C3  1  -0.12 12.011   ; 
qtot -0.42
 4   opls_158  1C4  1  -0.12 12.011   ; 
qtot -0.54
 5   opls_158  1C5  1  -0.12 12.011   ; 
qtot -0.66
 6   opls_157  1C6  1  -0.18 12.011   ; 
qtot -0.84
 7   opls_140  1H1  1   0.06  1.008   ; 
qtot -0.78
 8   opls_140  1H2  1   0.06  1.008   ; 
qtot -0.72
 9   opls_140  1H3  1   0.06  1.008   ; 
qtot -0.66
10   opls_140  1H4  1   0.06  1.008   ; 
qtot -0.6
11   opls_140  1H5  1   0.06  1.008   ; 
qtot -0.54
12   opls_140  1H6  1   0.06  1.008   ; 
qtot -0.48
13   opls_140  1H7  1   0.06  1.008   ; 
qtot -0.42
14   opls_140  1H8  1   0.06  1.008   ; 
qtot -0.36
15   opls_140  1H9  1   0.06  

RE: [gmx-users] grompp, energy minimization,, output file error

[Dallas B. Warren]

For starters there is no residue name in your .gro file, you simply have a 
number.  First column should be …

1HEX  C1
1HEX C2
.
.
.
1HEX H14
2HEX C1

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
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[gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Dear All
I am trying to study inter peptide interaction fpr which I need to put more
than one peptide in one simulation box. I did it with genconf command but
this inserts peptide in a regular ordered manner I want these to be in
irregular disordered insertion. Even after using genconf , I tried to
proceed furthe after solvation with spc water. The energy minimization
(steepest descent) failed to converge even after 5000 steps and theirafter
position restraint dynamics failed giving segmentation fault. Introducing
more peptide after generating .gro with -ci -nmol gives error showing more
than one residue in insert molecule.
Please help me and write  commands which I should follow.
Shahid Nayeem
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Re: [gmx-users] more than one peptide in one simulation box

[Mark Abraham]

On 23/04/10 13:16, shahid nayeem wrote:

Dear All
I am trying to study inter peptide interaction fpr which I need to put
more than one peptide in one simulation box. I did it with genconf
command but this inserts peptide in a regular ordered manner I want
these to be in irregular disordered insertion. Even after using genconf


Well that's a difficult and atypical scenario. genconf -shuffle will 
allow you to stack the same peptide in a regular array with random 
rotations of the whole box. Then you can solvate, equilibrate and run MD 
at a high temperature to give yourself a quasi-disordered starting state.



, I tried to proceed furthe after solvation with spc water. The energy
minimization (steepest descent) failed to converge even after 5000 steps
and theirafter position restraint dynamics failed giving segmentation
fault. Introducing more peptide after generating .gro with -ci -nmol
gives error showing more than one residue in insert molecule.
Please help me and write  commands which I should follow.


No, because that's an impossible task. We can't begin to guess the 
reasons for things failing without seeing the actual output (was the EM 
energy large and negative? what was the actual error message  from -ci 
-nmol?).


You should be careful to start with a small test case so that you can 
learn the workflow with a manageable problem. Can you get a single 
peptide to equilibrate? Two stacked peptides? It is best to learn to 
walk before trying to run :-)


Mark
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