[gmx-users] How to restrain ligand atom position

[Hitesh singla]

Dear all,

I have generated .itp file for ligand using PRODRG server which i included
in topology file. Now for position restrained dynamics, i wanted to restrain
atom positions for ligand and protein . But porse.itp which generated using
pdb2gmx contain restraints for protein only. Kindly provide me the solution
to restrain ligand atoms.

Thanks,
Hitesh Singla
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Re: [gmx-users] How to restrain ligand atom position

[Tsjerk Wassenaar]

Hi Hitesh,

The posre.itp file only contains a header [ position_restraints ]
followed by a list of atom numbers and restraint force constants.
Check chapter 5 of the manual for how and what. For a ligand it's
probably best to directly add the [ position_restraints  ] section in
the file with the [ molecule_type ] definition, possibly enclosed by
the statements #ifdef POSRES and #endif. Mind that the aom numbers
need to refer to the atom numbers within the molecule_type definition
and are not related to the atom numbers in the coordinate file.

Cheers,

Tsjerk

On Wed, Apr 15, 2009 at 9:05 AM, Hitesh singla
 wrote:
> Dear all,
>
> I have generated .itp file for ligand using PRODRG server which i included
> in topology file. Now for position restrained dynamics, i wanted to restrain
> atom positions for ligand and protein . But porse.itp which generated using
> pdb2gmx contain restraints for protein only. Kindly provide me the solution
> to restrain ligand atoms.
>
> Thanks,
> Hitesh Singla
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Implicit Solvent System - Energy Minimization

[Grace Tang]

Hello All,

I am doing energy minimization on a protein crystal structure to relax it.
 Afterwards, I plan to run md simulation with implicit solvent.  I am new at
this and have many questions.
1. Should the implicit solvent conditions be enabled when I run the energy
minimization?
2. What minimum potential energy should I expect (i know that when explicit
water is present, the energy often reaches -10E5 or -10E6)
3. What kind of emtol is appropriate?  Is it better to set it high so that
the system converges, or is it okay if machine precision is reached.

Below are 2 example runs I did with implicit_solvent = no
When I decreased the step size, the system did not converge anymore.  I was
wondering if this was due to chance, precision issues (I am using single
precision), or perhaps the emstep = 0.1 was reaching a nearby minimum and
0.01 was reaching the local minimum. Note, maximum force gets rather large
when convergence is to machine precision.

emtol= 1000
emstep   = 0.1
Steepest Descents converged to Fmax < 1000 in 29 steps
Potential Energy  = -4.9613008e+003
Maximum force = 6.4596338e+002 on atom 235
Norm of force = 1.0625026e+002

emtol= 1000
emstep   = 0.01
Steepest Descents converged to machine precision in 25 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -3.9642480e+003
Maximum force = 5.1200122e+003 on atom 416
Norm of force = 3.6602789e+002

Any advice is greatly appreciated.  Much thanks!
- Grace
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Re: [gmx-users] problem during inflatgro process

[Tsjerk Wassenaar]

Hi Nitu,

First of all, please try to use proper english for communication. This
way 'u don't make it EC-r 4 us'.
Second, you'd be better off getting some understanding of how
topologies and coordinate files are put together before trying to do
these things. A question like 'can I remove something from an .itp
file' is on the verge of being absurd. Of course you can. You just
have to make sure that you know what you are doing.

> [ molecules ]
> ; Name    number
> Protein_A   1
> Protein_B   1
> DMPC  119
> only the .itp file is present for protein and lipid
>

If you only have Protein(A,B) and DMPC in your system, then probably
the number of DMPC molecules is not what GROMACS sees in the topology
file (119). Check how many DMPC molecules are in your coordinate file
and decrease the numebr of DMPC molecules in the topology file.
However, I would strongly recommend doing some more reading first and
get some grips on the topology (file) format. Probably it wouldn't
hurt to follow some more tutorial material.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

[annalisa bordogna]

Hi,
I received a similar error during an equilibration by steepest descent in
which I had posed constraints on water, leaving the protein free to move.
I suggest to control your mdp file... maybe you did the same thing and the
system collapsed or exploded (you can see that reading the log file: if this
is the cause, you should see problems regarding water).

Cheers,
Annalisa

2009/4/13 Justin A. Lemkul 

>
>
> nam kim wrote:
>
>> process crashes around 100 steps out of 1000 requested.
>>
>>
> Fine, but you still haven't answered my question.  Do you receive any other
> messages?
>
> Do other systems run on the specific hardware you're using?  You may just
> have some instability in this particular system that is causing a crash.
>  Examine the  trajectory, see what's going wrong, and post any other
> relevant error messages, if you receive any.  Often times there is some
> output before a seg fault.
>
> -Justin
>
>
>  On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul 
>> wrote:
>>
>>>
>>> nam kim wrote:
>>>
 I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4).
 I have installed gromacs 4.0.4 two month ago and been working fine.
 Today, I just got Segment errors. Rebooting does not much help.

 Here is log:

 [rd:06790] *** Process received signal ***
 [d:06790] Signal: Segmentation fault (11)
 [rd:06790] Signal code:  (128)
 [rd:06790] Failing at address: (nil)
 [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430]
 [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496]
 [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e]
 [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a]
 [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552]
 [rd:06790] [ 5]
 /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0]
 [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32]
 [rd:06790] *** End of error message ***

  Are there any other messages from mdrun?  Anything printed to the
>>> screen
>>> (LINCS warnings, etc)?
>>>
>>> -Justin
>>>
>>>  Thanks
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  --
>>> 
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> 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
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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] Implicit Solvent System - Energy Minimization

[Mark Abraham]

Grace Tang wrote:

Hello All,

I am doing energy minimization on a protein crystal structure to relax 
it.  Afterwards, I plan to run md simulation with implicit solvent.  I 
am new at this and have many questions.
1. Should the implicit solvent conditions be enabled when I run the 
energy minimization?


No - while GROMACS has some vestiges in the user interface of an earlier 
attempt to implement implicit solvation simulations, these will not 
functional until at least version 4.1.


2. What minimum potential energy should I expect (i know that when 
explicit water is present, the energy often reaches -10E5 or -10E6)


Negative, and vaguely proportional to the number of atoms.

3. What kind of emtol is appropriate?  Is it better to set it high so 
that the system converges, or is it okay if machine precision is reached.  


It's pretty much irrelevant for preparing a system for MD. You'll have 
to equilibrate it later, and the value of an EM step is merely relieving 
any bad atom-atom contacts before they turn into huge accelerations. If 
the equilibration doesn't crash, you did enough EM.


Mark


Below are 2 example runs I did with implicit_solvent = no
When I decreased the step size, the system did not converge anymore.  I 
was wondering if this was due to chance, precision issues (I am using 
single precision), or perhaps the emstep = 0.1 was reaching a nearby 
minimum and 0.01 was reaching the local minimum. Note, maximum force 
gets rather large when convergence is to machine precision.


emtol= 1000
emstep   = 0.1
Steepest Descents converged to Fmax < 1000 in 29 steps
Potential Energy  = -4.9613008e+003
Maximum force = 6.4596338e+002 on atom 235
Norm of force = 1.0625026e+002

emtol= 1000
emstep   = 0.01
Steepest Descents converged to machine precision in 25 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -3.9642480e+003
Maximum force = 5.1200122e+003 on atom 416
Norm of force = 3.6602789e+002

Any advice is greatly appreciated.  Much thanks!
- Grace




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Re: [gmx-users] the position_restraints

[XAvier Periole]

You may have defined position restraints that exceed the number of atoms
present your system, or define them in a wrong manner.

Check manual and previous posts.

On Apr 15, 2009, at 12:29 AM, Justin A. Lemkul wrote:




He, Yang wrote:

HI Justin,
I just use the mdrun command and then get such error. Before that,  
I did not get other messages just go on well expect when I use the  
mdrun.
Also, when I did not use the position_restraints , it will run  
smoothly. As long as I add this even though the position_restraints  
includes only one atom, it will show the error.


This is difficult to diagnose exactly.  To me, removal of position  
restraints suggests that you are fixing in place some bad contact  
that is causing your system to crash.  Have a look at the trajectory  
to see what is going on.  Did EM work properly?  If you are still  
having trouble, post a more complete description of your system,  
relevant .mdp file(s), and anything else necessary to try to get a  
resolution.


-Justin


Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]  
On Behalf Of Justin A. Lemkul [jalem...@vt.edu]

Sent: Tuesday, April 14, 2009 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the position_restraints
He, Yang wrote:

HI all users,

I want to define the position_restraints in the itp file but when  
I run it, it always show that


Segmentation fault (core dumped)

You'll have to do better than "run it" - what do you mean, grompp?  
mdrun?
As written, your position restraints look OK, so I don't think the  
problem is
related to that section, necessarily.  How have you deduced that  
this is where

the problem lies?
Are you getting any other messages from (grompp? mdrun?) before the  
seg fault?

-Justin

and I will list the part below:

[position_restraints]
;ai funct fc
 111   1   1
 211   1   1
 311   1   1
 411   1   1
 511   1   1
 611   1   1
 711   1   1
 811   1   1
 911   1   1
1011   1   1
1111   1   1
1211   1   1
1311   1   1
1411   1   1
1511   1   1
1611   1   1
1711   1   1
1811   1   1
1911   1   1
2011   1   1
4111   1   1
4211   1   1
4311   1   1
4411   1   1
4511   1   1
4611   1   1
4711   1   1
4811   1   1
4911   1   1
5011   1   1
5111   1   1
5211   1   1
5311   1   1
5411   1   1
5511   1   1
5611   1   1
5711   1   1
5811   1   1
5911   1   1
6011   1   1

Can anyone of you tell me what is the problem for that?  Thank you  
very much in advance.


Yang
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--

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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
Graduate Research Assistant
ICTAS Doctoral Scholar
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] g_covar Segmentation fault

[Anirban Ghosh]

Hi ALL,

I have a system of beads with which I ran a CGMD (coarse grained MD) using 
NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I 
converted the trajectory in .trr format and made an index file of the entire 
system (45 beads). But now when I try to run g_covar using the group consisting 
the entire system, for least square fit and covariance analysis, it is giving 
Segmentation Fault. Am I doing anything wrong. Any suggestion is welcome.

Regards,

 
 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India


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Re: [gmx-users] g_covar Segmentation fault

[Mark Abraham]

Anirban Ghosh wrote:

Hi ALL,

I have a system of beads with which I ran a CGMD (coarse grained MD) 
using NAMD. Now I want to do a PCA analysis of this system using 
GROMACS. So I converted the trajectory in .trr format and made an index 
file of the entire system (45 beads). But now when I try to run g_covar 
using the group consisting the entire system, for least square fit and 
covariance analysis, it is giving Segmentation Fault. Am I doing 
anything wrong. Any suggestion is welcome.


Yes you're doing something wrong, but if you don't tell us at least your 
command line and your full output, how might we be expected to help? :-)


Mark
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Re: [gmx-users] g_covar Segmentation fault

[Nicolas]

Anirban Ghosh a écrit :

Hi ALL,

I have a system of beads with which I ran a CGMD (coarse grained MD) 
using NAMD. Now I want to do a PCA analysis of this system using 
GROMACS. So I converted the trajectory in .trr format
Convert a dcd file into a trr file is not that straightforward. How did 
you do that?
and made an index file of the entire system (45 beads). But now when I 
try to run g_covar using the group consisting the entire system, for 
least square fit and covariance analysis, it is giving Segmentation 
Fault. Am I doing anything wrong. Any suggestion is welcome.
You probably also need a tpr file. To create it, you need the parameters 
of your force field (in Gromacs format), the topology of each molecule 
you've got in your system (still in Gromacs format) and to run grompp.  
Depending on the original format of your force field, in can be quite 
difficult to do the file format conversion.


Hope that helps...
Nicolas


Regards,
 
 
*Anirban Ghosh*

*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*



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[gmx-users] Topologies and charges for large organic ligands

[Dean Cuebas]

Dear colleagues,

In 53a6, the topology and charges for (NAD+) nicotinamide adenine
dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
(without aromatic hydrogens).

Is there anyone who can tell me how such a molecule was charge group
parameterized? (with sufficient certainty to be included in the ff).

Please understand that I am not asking how to use the NAD topology that's
provided.

I've read that prodrg is a "good starting point" for parametrizing a ligand,
but what is the path to "improving" such a ligand from that starting point?
(the provided topology for NAD+ in the ff shows 17 charge groups with
an average of 3-4 atoms per charge group, whereas prodrg gives only 11
charge groups.)

I'm not concerned about angles and dihedrals, since that is pretty
painless... it's the charge groups that I'm concerned about.

In a nutshell, who and how was the final NAD+ parameters decided upon??
Does anyone know this??  Is it simply chemical intuition of estimated
charges that reproduce the dipole of the moiety (like an adenine ring), and
the charge groups contain the minimum number of atoms that reflect this?

Is there an algorithm to generating "improved" charge groups?

I ask these questions because my ligands are large organics... MW 800 and
greater.

Thanks for any and all help in this regard.

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancue...@smsu.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Southwest Missouri State University
Springfield, Missouri 65804



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Re: [gmx-users] Topologies and charges for large organic ligands

[Ran Friedman]

Hi,

The answer is (or should be) in:

@article{Oostenbrink2004,
   Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van
Gunsteren, W. F.},
   Title = {A biomolecular force field based on the free enthalpy of
hydration and solvation: The GROMOS force-field parameter sets 53A5 and
53A6},
   Journal = {J. Comput. Chem.},
   Volume = {25},
   Pages = {1656-1676},
   Year = {2004} }

Good luck,
Ran.

Dean Cuebas wrote:
> Dear colleagues,
>
> In 53a6, the topology and charges for (NAD+) nicotinamide adenine
> dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
> (without aromatic hydrogens).
>
> Is there anyone who can tell me how such a molecule was charge group
> parameterized? (with sufficient certainty to be included in the ff).
>
> Please understand that I am not asking how to use the NAD topology that's
> provided.
>
> I've read that prodrg is a "good starting point" for parametrizing a ligand,
> but what is the path to "improving" such a ligand from that starting point?
> (the provided topology for NAD+ in the ff shows 17 charge groups with
> an average of 3-4 atoms per charge group, whereas prodrg gives only 11
> charge groups.)
>
> I'm not concerned about angles and dihedrals, since that is pretty
> painless... it's the charge groups that I'm concerned about.
>
> In a nutshell, who and how was the final NAD+ parameters decided upon??
> Does anyone know this??  Is it simply chemical intuition of estimated
> charges that reproduce the dipole of the moiety (like an adenine ring), and
> the charge groups contain the minimum number of atoms that reflect this?
>
> Is there an algorithm to generating "improved" charge groups?
>
> I ask these questions because my ligands are large organics... MW 800 and
> greater.
>
> Thanks for any and all help in this regard.
>
>   

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[gmx-users] Problem with grompp?

[Hoof, B. van]

Hi everyone,

Since I am a new user of Gromacs, this problem is probably rather trivial, but 
I hope one of you would like to help me nonetheless. I have created a starting 
structure in a not very optimal situation, which I have then minimized. To 
continue, I would like to equilibrate the system further using leap-frog MD. To 
do so, I have used grompp in the following way:
grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10

This creates the following mdout.mdp: see attachment

Now as far as I can see, using the command `mdrun -v -c md_run.gro' should 
result in performing a 1,000,000 iteration md simulation of this system. 
However, when I issue that command, instead what I get is this:
>>>
 :-)  G  R  O  M  A  C  S  (-:

 Good ROcking Metal Altar for Chronical Sinners

:-)  VERSION 4.0.4  (-:


[...]

:-)  mdrun  (-:

Option Filename  Type Description

[...]

Getting Loaded...
Reading file topol.tpr, VERSION 4.0.4 (single precision)
Loaded with Money

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
Step=1, Dmax= 1.0e-02 nm, Epot=  1.23314e+20 Fmax= 2.04950e+19, atom= 11163
Step=2, Dmax= 1.2e-02 nm, Epot=  5.22616e+17 Fmax= 2.22256e+20, atom= 10863
Step=3, Dmax= 1.4e-02 nm, Epot=  1.46382e+17 Fmax= 7.52962e+17, atom= 10593
Step=4, Dmax= 1.7e-02 nm, Epot=  1.21703e+17 Fmax= 3.72098e+16, atom= 10331
Step=5, Dmax= 2.1e-02 nm, Epot=  2.22862e+16 Fmax= 4.87326e+18, atom= 10857
Step=6, Dmax= 2.5e-02 nm, Epot=  1.09032e+16 Fmax= 4.39937e+15, atom= 15106
Step=7, Dmax= 3.0e-02 nm, Epot=  1.81517e+15 Fmax= 6.07049e+14, atom= 15230
Step=8, Dmax= 3.6e-02 nm, Epot=  2.84750e+14 Fmax= 9.82848e+14, atom= 14675
Step=9, Dmax= 4.3e-02 nm, Epot=  2.33131e+14 Fmax= 2.39469e+13, atom= 11419
Step=   10, Dmax= 5.2e-02 nm, Epot=  7.23189e+12 Fmax= 2.72305e+14, atom= 14565
Step=   11, Dmax= 6.2e-02 nm, Epot=  3.19510e+12 Fmax= 4.82192e+12, atom= 10638
Step=   13, Dmax= 3.7e-02 nm, Epot=  1.82616e+12 Fmax= 1.11184e+13, atom= 11929
[... etc.]
<<<

This is a minimization using the steepest descent algorithm. What am I doing 
wrong here?

Thank you in advance for your kind help!

Greetings,
Bram van Hoof






mdout.mdp
Description: mdout.mdp
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Re: [gmx-users] Problem with grompp?

[Justin A. Lemkul]

Hoof, B. van wrote:

Hi everyone,

Since I am a new user of Gromacs, this problem is probably rather trivial, but 
I hope one of you would like to help me nonetheless. I have created a starting 
structure in a not very optimal situation, which I have then minimized. To 
continue, I would like to equilibrate the system further using leap-frog MD. To 
do so, I have used grompp in the following way:
grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10

This creates the following mdout.mdp: see attachment

Now as far as I can see, using the command `mdrun -v -c md_run.gro' should 
result in performing a 1,000,000 iteration md simulation of this system. 
However, when I issue that command, instead what I get is this:
 :-)  G  R  O  M  A  C  S  (-:

 Good ROcking Metal Altar for Chronical Sinners

:-)  VERSION 4.0.4  (-:


[...]

:-)  mdrun  (-:

Option Filename  Type Description

[...]

Getting Loaded...
Reading file topol.tpr, VERSION 4.0.4 (single precision)
Loaded with Money

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
Step=1, Dmax= 1.0e-02 nm, Epot=  1.23314e+20 Fmax= 2.04950e+19, atom= 11163
Step=2, Dmax= 1.2e-02 nm, Epot=  5.22616e+17 Fmax= 2.22256e+20, atom= 10863
Step=3, Dmax= 1.4e-02 nm, Epot=  1.46382e+17 Fmax= 7.52962e+17, atom= 10593
Step=4, Dmax= 1.7e-02 nm, Epot=  1.21703e+17 Fmax= 3.72098e+16, atom= 10331
Step=5, Dmax= 2.1e-02 nm, Epot=  2.22862e+16 Fmax= 4.87326e+18, atom= 10857
Step=6, Dmax= 2.5e-02 nm, Epot=  1.09032e+16 Fmax= 4.39937e+15, atom= 15106
Step=7, Dmax= 3.0e-02 nm, Epot=  1.81517e+15 Fmax= 6.07049e+14, atom= 15230
Step=8, Dmax= 3.6e-02 nm, Epot=  2.84750e+14 Fmax= 9.82848e+14, atom= 14675
Step=9, Dmax= 4.3e-02 nm, Epot=  2.33131e+14 Fmax= 2.39469e+13, atom= 11419
Step=   10, Dmax= 5.2e-02 nm, Epot=  7.23189e+12 Fmax= 2.72305e+14, atom= 14565
Step=   11, Dmax= 6.2e-02 nm, Epot=  3.19510e+12 Fmax= 4.82192e+12, atom= 10638
Step=   13, Dmax= 3.7e-02 nm, Epot=  1.82616e+12 Fmax= 1.11184e+13, atom= 11929
[... etc.]
<<<

This is a minimization using the steepest descent algorithm. What am I doing 
wrong here?

Thank you in advance for your kind help!



If you use default names (i.e., topol.tpr for output), you can easily confuse 
yourself and wind up running the wrong input file.  The mdout.mdp file you 
posted should correspond to MD; most likely you've just re-run the same .tpr 
file that you used for minimization.


-Justin


Greetings,
Bram van Hoof








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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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] Implicit Solvent System - Energy Minimization

[Grace Tang]

Sorry, I wasn't too clear in the first message.  I will be using OpenMM
Gromacs, which does support implicit solvent.  My current energy
minimization steps only lower the energy to -5E3.  Is this okay considering
water is not around?
Is is necessary to do equilibration if I am using implicit solvent?  Is so,
can anyone direct me to reasonable parameters?

Thanks!
Grace


On Wed, Apr 15, 2009 at 2:55 AM, Mark Abraham wrote:

> Grace Tang wrote:
>
>> Hello All,
>>
>> I am doing energy minimization on a protein crystal structure to relax it.
>>  Afterwards, I plan to run md simulation with implicit solvent.  I am new at
>> this and have many questions.
>> 1. Should the implicit solvent conditions be enabled when I run the energy
>> minimization?
>>
>
> No - while GROMACS has some vestiges in the user interface of an earlier
> attempt to implement implicit solvation simulations, these will not
> functional until at least version 4.1.
>
>  2. What minimum potential energy should I expect (i know that when
>> explicit water is present, the energy often reaches -10E5 or -10E6)
>>
>
> Negative, and vaguely proportional to the number of atoms.
>
>  3. What kind of emtol is appropriate?  Is it better to set it high so that
>> the system converges, or is it okay if machine precision is reached.
>>
>
> It's pretty much irrelevant for preparing a system for MD. You'll have to
> equilibrate it later, and the value of an EM step is merely relieving any
> bad atom-atom contacts before they turn into huge accelerations. If the
> equilibration doesn't crash, you did enough EM.
>
> Mark
>
>  Below are 2 example runs I did with implicit_solvent = no
>> When I decreased the step size, the system did not converge anymore.  I
>> was wondering if this was due to chance, precision issues (I am using single
>> precision), or perhaps the emstep = 0.1 was reaching a nearby minimum and
>> 0.01 was reaching the local minimum. Note, maximum force gets rather large
>> when convergence is to machine precision.
>>
>> emtol= 1000
>> emstep   = 0.1
>> Steepest Descents converged to Fmax < 1000 in 29 steps
>> Potential Energy  = -4.9613008e+003
>> Maximum force = 6.4596338e+002 on atom 235
>> Norm of force = 1.0625026e+002
>>
>> emtol= 1000
>> emstep   = 0.01
>> Steepest Descents converged to machine precision in 25 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy  = -3.9642480e+003
>> Maximum force = 5.1200122e+003 on atom 416
>> Norm of force = 3.6602789e+002
>>
>> Any advice is greatly appreciated.  Much thanks!
>> - Grace
>>
>>
>> 
>>
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[gmx-users] improper dihedrals for OPLS

[parksh]

Dear gmx-users,

I am confused about the exact formula for improper OPLS dihedrals in gromacs.
Is it periodic, e.g. V[1-cos(2x)], or harmonic, e.g. [V*(x-x0)^2]?
In ffoplsaa.rtp, it says in the Col 4 in the following the type of improper 
dihedrals to be 1,
which I believe is a harmonic function. The gromacs manual says the same.

[ bondedtypes ]
; Col 1: Type of bond 
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
 1   1  3  11 3  1 0

Meanwhile, in ffoplsaabon.itp, it appears that the periodic function, not 
harmonic, is used for
improper dihedrals, as shown in the following:

[ dihedraltypes ]
; Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use impropers for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), the are actually
; implemented as proper dihedrals [1+cos(2*x+180)] for the moment, 
; to keep things compatible.
; The defines are used in ffoplsaa.rtp or directly in your .top ile.

Which one is correct? Periodic or harmonic? And what does each number in 
improper dihedral
parameters mean? For example, what do 180.0, 43.93200, and 2 mean in the 
following improper
dihedral parameters?

#define improper_O_C_X_Y180.0 43.93200   2

Many thanks in advance for your help!

Best,
Sung


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Re: [gmx-users] Implicit Solvent System - Energy Minimization

[Mark Abraham]

Grace Tang wrote:
Sorry, I wasn't too clear in the first message.  I will be using OpenMM 
Gromacs, which does support implicit solvent.  
My current energy minimization steps only lower the energy to -5E3.  Is 
this okay considering water is not around?


Probably.

Is is necessary to do equilibration if I am using implicit solvent?  


Yes. Generated velocities on an arbitrary starting structure will not 
necessarily be in the correct thermodynamic ensemble.


> Is

so, can anyone direct me to reasonable parameters?


Parameters for what? You should be looking closely at the documentation 
for OpenMM, and the methods in whatever publications they may have made 
using it. If they haven't published, and you aren't in close contact 
with them, then you should reconsider your choice of software. The kind 
of science you want to do should usually drive that choice.


Mark
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[gmx-users] Re: gmx-users Digest, Vol 60, Issue 89

[Anirban Ghosh]

ser interface of an earlier 
attempt to implement implicit solvation simulations, these will not 
functional until at least version 4.1.

> 2. What minimum potential energy should I expect (i know that when 
> explicit water is present, the energy often reaches -10E5 or -10E6)

Negative, and vaguely proportional to the number of atoms.

> 3. What kind of emtol is appropriate?  Is it better to set it high so 
> that the system converges, or is it okay if machine precision is reached.  

It's pretty much irrelevant for preparing a system for MD. You'll have 
to equilibrate it later, and the value of an EM step is merely relieving 
any bad atom-atom contacts before they turn into huge accelerations. If 
the equilibration doesn't crash, you did enough EM.

Mark

> Below are 2 example runs I did with implicit_solvent = no
> When I decreased the step size, the system did not converge anymore.  I 
> was wondering if this was due to chance, precision issues (I am using 
> single precision), or perhaps the emstep = 0.1 was reaching a nearby 
> minimum and 0.01 was reaching the local minimum. Note, maximum force 
> gets rather large when convergence is to machine precision.
> 
> emtol= 1000
> emstep   = 0.1
> Steepest Descents converged to Fmax < 1000 in 29 steps
> Potential Energy  = -4.9613008e+003
> Maximum force = 6.4596338e+002 on atom 235
> Norm of force = 1.0625026e+002
> 
> emtol= 1000
> emstep   = 0.01
> Steepest Descents converged to machine precision in 25 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -3.9642480e+003
> Maximum force = 5.1200122e+003 on atom 416
> Norm of force = 3.6602789e+002
> 
> Any advice is greatly appreciated.  Much thanks!
> - Grace
> 
> 
> 
> 
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--

Message: 2
Date: Wed, 15 Apr 2009 18:12:32 +0530 (IST)
From: Anirban Ghosh 
Subject: [gmx-users] g_covar Segmentation fault
To: GROMACS 
Message-ID: <1093.26419...@web8504.mail.in.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi ALL,

I have a system of beads with which I ran a CGMD (coarse grained MD) using 
NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I 
converted the trajectory in .trr format and made an index file of the entire 
system (45 beads). But now when I try to run g_covar using the group consisting 
the entire system, for least square fit and covariance analysis, it is giving 
Segmentation Fault. Am I doing anything wrong. Any suggestion is welcome.

Regards,



Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India


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Message: 3
Date: Wed, 15 Apr 2009 22:48:51 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] g_covar Segmentation fault
To: Discussion list for GROMACS users 
Message-ID: <49e5d7b3.3030...@anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed

Anirban Ghosh wrote:
> Hi ALL,
> 
> I have a system of beads with which I ran a CGMD (coarse grained MD) 
> using NAMD. Now I want to do a PCA analysis of this system using 
> GROMACS. So I converted the trajectory in .trr format and made an index 
> file of the entire system (45 beads). But now when I try to run g_covar 
> using the group consisting the entire system, for least square fit and 
> covariance analysis, it is giving Segmentation Fault. Am I doing 
> anything wrong. Any suggestion is welcome.

Yes you're doing something wrong, but if you don't tell us at least your 
command line and your full output, how might we be expected to help? :-)

Mark


--

Message: 4
Date: Wed, 15 Apr 2009 15:02:55 +0200
From: Nicolas 
Subject: Re: [gmx-users] g_covar Segmentation fault
To: Discussion list for GROMACS users 
Message-ID: <49e5daff.2000...@ucalgary.ca>
Content-Type: text/plain; charset="utf-8"

Anirban Ghosh a écrit :
> Hi ALL,
>
> I have a system of beads with which I ran a CGMD (