[gmx-users] g_dist

[Alessandro Mattozzi]

Title: g_dist






Hi all
how reacts g_dist if one group contents 3 segments of three identical molecules. Are the distances calculated referring to the centers of mass of the single molecules segments and then averaged or referring to the center of mass of the set of the three segments?
Regards

Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden





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[gmx-users] grompp problem

[leila_ayadi]

 encountered the problem when running grompp:
Fatal error : number of coordinates in coordinate file calsm.pdb,134637
does not match topology  cals.top,0


the em.mdp file is as follows :
;
;  User spoel (236)
;  Wed Nov 3 17:12:44 1993
;  Input file
;


constraints = none
integrator = steep
nsteps = 100
;
;  Energy minimizing stuff
;
emtol = 2000
emstep = 0.01

nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no



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[gmx-users] MD run end abnormally more detailed info

[主月 ：）]

Hi :
Mark, thanks for your advice.

But i only use the single-processor.And the 
enviourment is RedHat 9.0 with gromacs 3.3.1.

what is other problem of this 
error

Date: Sun, 2 Jul 2006 15:17:53 +1000 (EST)From: "Mark Abraham" [EMAIL PROTECTED]Subject: 
Re: [gmx-users] MD run end abnormallyTo: "Discussion list for GROMACS users" 
gmx-users@gromacs.orgMessage-ID:[EMAIL PROTECTED]Content-Type: 
text/plain;charset=iso-8859-1 Hi: I install GMX FFTW 
MPI in my own folders. And then i used a begin structure which performed 
well at other computers to test the GMX programme. What 
is strange to me is that the job can run well at begginning time but 
after a while the CPU was not still busy, and the output file was not 
change. I chencked the log file. There is no reason. And i used g_energy 
to check the condition of MD.But the "Potential"Kinetic En." 
"Temperature" were all in equilibrium. Every time the error came 
with different step. Some time is 5 step. Some time is 2445001 
. What is the error? How can i fix it.It sounds like you 
are using a Windows MPI environment that isn't workingproperly. Test 
single-processor calculations to see they work OK. If so,try to eliminate 
other processes running on the machines, and turn off anyauto-hibernation 
stuff.Mark


祝 

好

*Ji 
Qing（吉青）Institute of Chemistry, Chinese Academy of 
Sciences（中科院化学所）Tel: 0086-10-62562894 
，82618423*


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Re: [gmx-users] grompp problem

[jahanshah ashkani]

Hi, Do you have any temp.top in your folder where you ran genbox? If is yes, you can use it instead of cals.top.[EMAIL PROTECTED] wrote:   encountered the problem when running grompp:Fatal error : number of coordinates in coordinate file does not match topology the em.mdp file is as follows :;; User spoel (236); Wed Nov 3 17:12:44 1993; Input file;constraints = noneintegrator = steepnsteps = 100;; Energy minimizing stuff;emtol = 2000emstep = 0.01nstcomm = 1ns_type = gridrlist = 1rcoulomb = 1.0rvdw = 1.0Tcoupl = noPcoupl = nogen_vel = no___Tiscali Broadband from 14.99 with free
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Re: [gmx-users] Scripting Analysis tools in tcsh

[Olli Lehtonen]

On Fri, 30 Jun 2006, Arneh Babakhani wrote:

 Hello GMX users,

 (this may be more of a tcsh question, but here goes anyway).

 I'm trying to write a script to go through some trajectories and
 calculate hbonding.  It looks like this:

 #!/bin/tcsh
 foreach number (1 2 3 4 5 6 7 8 9 10 11)
 g_hbond -f ../../FullMD/FullMD$number.trr -s
 ../../FullMD/FullMD$number.tpr -num hbnum-all-$number +
  1
  12
  +
 end

You are probably having an extra space in front of the latter + sign. Now
+ and end are considered as input for g_hbond.

Olli

PS. For general shell script questions a newsgroup like comp.unix.shell is
a good place to keep in mind.
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Re: [gmx-users] grompp problem

[leila_ayadi]

I used the temp.top instead of cals.top and i found the same message :
number of coordinates in coordinate file cals.pdb,134637 does not match
topology temp.top,0 although the temp.top is not empty.
I run gromacs on windows.
-- Original Message --
Date: Sun, 2 Jul 2006 09:14:53 -0700 (PDT)
From: jahanshah ashkani [EMAIL PROTECTED]
Subject: Re: [gmx-users] grompp problem
To: Discussion list for GROMACS users gmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org


Hi, Do you have any temp.top in your folder where you ran genbox? If is
yes,
you can use it instead of cals.top.

[EMAIL PROTECTED] wrote:   encountered the problem when running grompp:
Fatal error : number of coordinates in coordinate file
does not match topology


the em.mdp file is as follows :
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;


constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01

nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no



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[gmx-users] oplsaa force field

[Dongsheng Zhang]

Dear GMX users,

I'd like to use oplsaa FF format to build my own force field for my
project. After I finished it, I can use pdb2gmx. but not grompp. The
problem is from my **nb.itp file. I have specified some unusual (not
follow the combination rule) nonbonded interaction parameters after
[ atomtypes ] section as follows:

 [ nonbond_params ]
; ij func  sigma  epsilon
CTCT  13.8e-01  2.09200e-01

When I run grompp, the program complains that atom type CT is not found.
If I change CT to opls_182, then it works fine. However, when I check
oplsaabon.itp, CT is used, but not opls_182. Could anyone tell me why I
can't use atom type in *nb.itp? How can I fix it? If opls_182 is defined
as atom type, then how does gromacs recognize CT is **bon.itp?


By the way, my question relates to my previous question. Unfortunately,
no one answered it. I really appreciate someone can help me. The
following is my previous email:

In ffoplsaanb.itp, there are 8 columns.
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_001   C   6  12.01100 0.500   A3.75000e-01
4.39320e-01 ; SIG

In ffG53a5nb.itp, there are 7 columns.
[ atomtypes ]
;name  at.num   mass  charge ptype   c6   c12
O8  0.000  0.000 A  0.0022619536   1e-06

Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF,
but 7 columns for gromos FF? Thanks!

All the best!


Dongsheng


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[gmx-users] LINCS warning

[Vanessa Oklejas]

Hi everyone,

I'm having trouble with performing 1 ns simulations on a 318 residue 
long protein with 'mdrun'. The run.log file, included at the end of 
this message, gives a 'LINCS warning' within a minute or two after 
the simulation begins:


Step 148, time 0.296 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.151505 (between atoms 4353 and 4355) rms 0.002175
bonds that rotated more than 60 degrees:

I've have been minimizing the structure of the protein prior to 
trying to perform the simulation (no problems here). Also, when I use 
'grompp' to produce a .tpr file for a 1 ns MD simulation with the 
minimized structure, I have no problems with this either. The .mdp 
file that is fed into the .tpr file will work with different protein 
structures (single residue mutants) without incident. So, it would 
appear that the .mdp file used to compile the .tpr file is working.


What is really puzzling to me is that the simulation will sometimes 
run properly and sometimes it won't even though it would appear 
that  I use the exact same .gro file.  Does this sound familiar to anyone?


Thanks,
Vanessa


Reading file 1_T114A_F.tpr, VERSION 3.1.4 (single precision)
Reading file 1_T114A_F.tpr, VERSION 3.1.4 (single precision)
starting mdrun 'hALDR2 (060425 pH=6.5) w/ F inhibitor implicit water'
50 steps,   1000.0 ps.


Step 148, time 0.296 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.151505 (between atoms 4353 and 4355) rms 0.002175
bonds that rotated more than 60 degrees:
bonds that rotated more than 60 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4353   4355   90.30.1010   0.1163  0.1010

Step 148, time 0.296 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.150984 (between atoms 4353 and 4355) rms 0.002227
bonds that rotated more than 60 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4353   4355   90.00.1010   0.1162  0.1010

Step 149, time 0.298 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.053408 (between atoms 4353 and 4355) rms 0.000836
bonds that rotated more than 60 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4353   4355   89.60.1162   0.1064  0.1010

Step 149, time 0.298 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.049700 (between atoms 4353 and 4355) rms 0.000769
bonds that rotated more than 60 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 atom 1 atom 2  angle  previous, current, constraint length
   4353   4355   90.00.1162   0.1060  0.1010

Step 150, time 0.3 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 166995.593750 (between atoms 4348 and 4350) rms 3256.995850
bonds that rotated more than 60 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4329   4331   65.30.1449   2.0483  0.1449
   4331   4332   75.60.1090   2.0105  0.1090
   4331   4333   64.60.1526   2.0440  0.1526
   4331   4342   68.60.1522   9.4604  0.1522
   4342   4343   68.40.1229   9.5175  0.1229
   4342   4344   74.80.1335  33.8721  0.1335
   4344   4345   79.40.1010  31.1369  0.1010
   4344   4346   85.90.1450 170.9566  0.1449
   4346   4347   86.50.1090 151.5872  0.1090
   4346   4348   88.90.1527 774.3875  0.1526
   4346   4356   84.60.1523 164.2752  0.1522
   4348   4349   89.50.1091 647.3028  0.1090
   4348   4350   90.00.1092 18202.6279  0.1090
   4348   4351   89.70.1527 957.9619  0.1522
   4351   4352   89.60.1234 262.4561  0.1229
   4351   4352   89.60.1234 262.4561  0.1229
   4351   4353   90.50.1355 1149.1741  0.1335
   4353   4354   89.70.1007 178.1642  0.1010
   4353   4355   90.00.1060 16749.2714  0.1010
   4356   4357   76.10.1229  38.4753  0.1229
   4356   4358   73.10.1335  39.2402  0.1335
   4358   4359   69.50.1010   9.6261  0.1010
   4358   4360   69.70.1449  10.2906  0.1449
   4360   4361   72.90.1090   2.6064  0.1090
   4360   4362   69.10.1526   2.6707  0.1526
   4360   4376   63.90.1522   2.6586  0.1522
Wrote pdb files with previous and current coordinates

Step 150, time 0.3 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 166882.437500 (between atoms 4348 and 4350) rms 3256.037109
bonds that rotated more than 60 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4319   4321   77.00.1449   0.2666  0.1449
   4321   4322   78.40.1090   0.1816  0.1090
   4321   4323   72.40.1526   0.2694  0.1526
   4321   4327   69.10.1522   0.3681  0.1522
   4327   4328   73.50.1229   0.4389  0.1229
 4327   4328   73.50.1229   0.4389  0.1229
   4327   4329   80.00.1335   1.6753  0.1335
   4329   4330   80.90.1010   1.3435  0.1010
   

Re: [gmx-users] MD run end abnormally more detailed info

[Mark Abraham]

 Hi :
 Mark, thanks for your advice.

 But i only use the single-processor.And the enviourment is RedHat 9.0 with
 gromacs 3.3.1.

OK that should be less problematic. If you are using a single-processor
MPI environment, check that you've configured (and started!) that
correctly. Preferably try a non-MPI single-processor calculation to test.

Mark

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Re: [gmx-users] oplsaa force field

[Mark Abraham]

The answers to both of these questions are in the comments in
src/kernel/toppush.c, in function push_at(). I found them grepping
src/*/*.[ch] for scanf (the C function you'd use to read up these files)
and looking for topology-related filenames...

 I'd like to use oplsaa FF format to build my own force field for my
 project. After I finished it, I can use pdb2gmx. but not grompp. The
 problem is from my **nb.itp file. I have specified some unusual (not
 follow the combination rule) nonbonded interaction parameters after
 [ atomtypes ] section as follows:

  [ nonbond_params ]
 ; ij func  sigma  epsilon
 CTCT  1  3.8e-01  2.09200e-01

 When I run grompp, the program complains that atom type CT is not found.
 If I change CT to opls_182, then it works fine. However, when I check
 oplsaabon.itp, CT is used, but not opls_182. Could anyone tell me why I
 can't use atom type in *nb.itp? How can I fix it? If opls_182 is defined
 as atom type, then how does gromacs recognize CT is **bon.itp?

OPLS/AA appears to use different names for bonded and non-bonded atom types.
 See line 172 of the above file.

 By the way, my question relates to my previous question. Unfortunately,
 no one answered it. I really appreciate someone can help me. The
 following is my previous email:

 In ffoplsaanb.itp, there are 8 columns.
 ; name  bond_typemasscharge   ptype  sigma  epsilon
  opls_001   C   6  12.01100 0.500   A3.75000e-01
 4.39320e-01 ; SIG

 In ffG53a5nb.itp, there are 7 columns.
 [ atomtypes ]
 ;name  at.num   mass  charge ptype   c6   c12
 O8  0.000  0.000 A  0.0022619536   1e-06

 Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF,
 but 7 columns for gromos FF? Thanks!

The algorithm is described just below in that file too.

Mark

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Re: [gmx-users] LINCS warning

[Mark Abraham]

 Hi everyone,

 I'm having trouble with performing 1 ns simulations on a 318 residue
 long protein with 'mdrun'. The run.log file, included at the end of
 this message, gives a 'LINCS warning' within a minute or two after
 the simulation begins:

 Step 148, time 0.296 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 max 0.151505 (between atoms 4353 and 4355) rms 0.002175
 bonds that rotated more than 60 degrees:

In plain English, this means the bond or angle constraints implemented
with the LINCS algorithm are having to be enforced after very large
deviations. This suggests that there is something numerically unstable
going on. Visualising the trajectory is always a good idea at this point,
as it can suggest whether the whole world is exploding (re-visit the
preparation protocol) or just part of it (be more cunning).

 I've have been minimizing the structure of the protein prior to
 trying to perform the simulation (no problems here). Also, when I use
 'grompp' to produce a .tpr file for a 1 ns MD simulation with the
 minimized structure, I have no problems with this either. The .mdp
 file that is fed into the .tpr file will work with different protein
 structures (single residue mutants) without incident. So, it would
 appear that the .mdp file used to compile the .tpr file is working.

Yes... the .mdp file describes the conduct of the simulation, the .top
file describes the topology of system, and the structure (.gro) file
describes the original conformation. All three are combined to produce the
.tpr file. There are some constraints on the three, but subject to those
constraints you can swap different .mdp/.top/.gro files.

 What is really puzzling to me is that the simulation will sometimes
 run properly and sometimes it won't even though it would appear
 that  I use the exact same .gro file.  Does this sound familiar to anyone?

There is more needed to prepare a system for MD than energy minimization
to relieve bad contacts. Read any MD paper and they will describe some
kind of regime for generating initial velocities and heating the system to
the required temperature, and then leave it to sit for a while. Often
temperatures will be equilibrated in NVT, before relaxing to NPT when that
ensemble is desired for the production calculation. Since you don't
describe doing this, my guess is that you are not doing it (well enough).

Mark

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Re: [gmx-users] grompp problem

[jahanshah ashkani]

I didn’t find ccp address in your em.mdp file. Please add ccp.exe to your folder where you will run grompp and add following sentence to em.mdp file  cpp = cpp[EMAIL PROTECTED] wrote:  I used the temp.top instead of cals.top and i found the same message :number of coordinates in coordinate file does not matchtopology although the temp.top is not empty.I run gromacs on windows.-- Original Message --Date: Sun, 2 Jul 2006 09:14:53
 -0700 (PDT)From: jahanshah ashkani <[EMAIL PROTECTED]>Subject: Re: [gmx-users] grompp problemTo: Discussion list for GROMACS users Reply-To: Discussion list for GROMACS users Hi, Do you have any temp.top in your folder where you ran genbox? If isyes,you can use it instead of cals.top.[EMAIL PROTECTED] wrote: encountered the problem when running grompp:Fatal error : number of coordinates in coordinate filedoes not match topologythe em.mdp file is as follows :;; User spoel (236); Wed Nov 3 17:12:44 1993; Input file;constraints = noneintegrator = steepnsteps = 100;; Energy minimizing stuff;emtol = 2000emstep = 0.01nstcomm = 1ns_type = gridrlist =
 1rcoulomb = 1.0rvdw = 1.0Tcoupl = noPcoupl = nogen_vel = no___Tiscali Broadband from 14.99 with free setup!http://www.tiscali.co.uk/products/broadband/___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php __Do You Yahoo!?Tired of spam? Yahoo! Mail has the best spam protection aroundhttp://mail.yahoo.com___gmx-users mailing list
 gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php___Tiscali Broadband from 14.99 with free setup!http://www.tiscali.co.uk/products/broadband/___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php __Do You Yahoo!?Tired of spam?  Yahoo! Mail has the best spam protection around
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[gmx-users] Hbond dynamic representation in MD movie

[raja]

Hi all,
Is there a tool known for displaying hbonds dynamically during gromacs
trajectory visualization process and should also have facility to make
MD movie out of it.

With thanks!
B.Nataraj

-- 
  raja
  [EMAIL PROTECTED]

-- 
http://www.fastmail.fm - A no graphics, no pop-ups email service

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Re: [gmx-users] Hbond dynamic representation in MD movie

[Mark Abraham]

 Hi all,
 Is there a tool known for displaying hbonds dynamically during gromacs
 trajectory visualization process and should also have facility to make
 MD movie out of it.

VMD http://www.ks.uiuc.edu/Research/vmd/

Mark

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Re: [gmx-users] query about protein-ligand complex

[sangeeta]

I could not mail you as our net was down, 
you asked me Is your system
 properly minimized? 
My question is how can I understand whether my system is properly minimised?
  the run is still going on, I can realize that something is going wrong. 
But I can not detect it.The log file is giving the error that the system is 
not properly minimised.I am giving you the messege,
2127   2131  176.6  223178260480. 3921810030592.  0.1330
   2128   2129  176.6  69075034112. 1233987043328.  0.1000
   2128   2130  176.6  69075394560. 1233986912256.  0.1000
   2131   2132  176.5  69056528384. 1233902108672.  0.1000
   2131   2133  176.5  69054996480. 1233896734720.  0.1000
Constraint error in algorithm Lincs at step 9
 
t = 0.018 ps: Water molecule starting at atom 13339 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Large VCM(group rest): -168597.92188, 112023.07031, -175543.56250, ekin-cm:  
3.95206e+15

 will you please give  me some suggestion , so that 
I can run the system from the beginning?
regards
Sangeeta


On Fri, 30 Jun 2006 14:50:44 +0200, Erik Marklund wrote
 On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote:
  
  Dear all,
  
  I am trying to run the dynamics of protein-ligand complex following the 
  tutorial GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1
  . I am running position restricted dynamics of the 91az8.pdb protein as 
  mentioned in the tutorial trp.pdb  drg.pdb)in a Linux server machine, I 
can 
  not understand why it is taking such a long time, the machine is not 
busy 
  with any other jobs.I ran it before  I stopped  the run at 1200 min, 
now it 
  is going for about 215 min,   step6.pdb, step7.pdb etc files are being 
  formed, I can not undersyand whether I am doing any wrong step, why it 
is 
  taking such a long time , I don't know , please help.
 
 stepX.pdb files are generated when things go wrong, for example when
 forces or other quantities becomes NaN or Inf. The log files should give
 some clues about what is happening to your system.Is your system
 properly minimized?  Please provide some more information, otherwise it's
 difficult to help you.
 
 /Erik Marklund
 
  
  regards
  sangeeta 
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 -- 
 Erik Marklund, PhD Student, Molecular Biopcysics group,
 Dept. of Cell and Molecular Biology, Uppsala University.
 Husargatan 3, Box 596,  75124 Uppsala, Sweden
 phone:  46 18 471 4537  fax: 46 18 511 755
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