[gmx-users] Water molecule can not be settled - mdrun error
Lara Bunte
lara.bunte at yahoo.de
Mon Sep 24 22:57:16 CEST 2012
Hi
How to make the energy minimization in double precision? Do this mean to use grompp twice?
I changed in my energy minimization I changed emtol from 1000 to 100 and got:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+02
Number of steps = 5000
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100
Steepest Descents converged to machine precision in 355 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -1.3305919e+05
Maximum force = 3.6814004e+03 on atom 19
Norm of force = 6.2041531e+01
Is this good or bad?
I also changed my .mdp file for the equilibration of the water around the flavin with the right cut-offs. Now it looks like this:
define = -DPOSRES
integrator = md
dt = 0.002
emtol = 1000.0
emstep = 0.01
nsteps = 5000
nstlist = 1
rlist = 1.2
rlistlong = 1.4
rcoulomb = 1.2
coulombtype = pme
vdw-type = switch
rvdw_switch = 0.8
rvdw = 1.2
nstxout = 100
nstvout = 100
nstenergy = 100
nstlog = 100
tcoupl = V-rescale
tc-grps = ISO SOL
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = no
Is this okay now? I have a further question about that. As far as I understand I want to equilibrate the water around the lumiflavin which is again a kind of minimization. Why do I have to use the integrator md and not steep like in the minimization before? I use integrator md and also DPOSRES because my tutorial says I have to use this by I asked myself why not steep?
Sadly with this settings I am again at the problem from the beginning of our discussion.
step 266: Water molecule starting at atom 4416 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
I hope that understanding more about this minimization stuff will help me to fix this. I am interested what could be now a problem in the .mdp file.
Thanks for helping me
Greetings
Lara
----- Ursprüngliche Message -----
Von: Justin Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
CC:
Gesendet: 18:34 Montag, 24.September 2012
Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
On 9/24/12 12:31 PM, Peter C. Lai wrote:
> As I noted before, you can safely ignore the gromacs notices when setting
> them to the correct cutoffs I listed.
>
Agreed. Please use the cutoffs that have been posted explicitly 3-4 times now.
> Your energy minimization still looks a bit high (1000)...
>
> Justin might have some more ideas...
>
The maximum force is too high. If this condition persists with the proper
cutoffs, then the topology is to blame. You've yet to explain where the
parameters for lumiflavin came from, but if forces are high and the simulations
collapse, then the parameterization is likely insufficiently accurate.
-Justin
> On 2012-09-24 05:07:59PM +0100, Lara Bunte wrote:
>> Hi
>>
>> The result of the energy minimization before is:
>>
>> Steepest Descents:
>> Tolerance (Fmax) = 1.00000e+03
>> Number of steps = 5000
>>
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 1000
>>
>> Double precision normally gives you higher accuracy.
>> You might need to increase your constraint accuracy, or turn
>> off constraints alltogether (set constraints = none in mdp file)
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 226 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy = -1.3277053e+05
>> Maximum force = 1.7070897e+03 on atom 8
>> Norm of force = 3.8431282e+01
>>
>> My System is lumiflavin in water, tip3p water model and charmm27 force field. My actual goal is to equilibrate the water around the lumiflavin with that .mdp file I wrote. What is now wrong with the cut-offs? If I use the settings for charmm27 cut-offs you wrote I got all that problems I wrote. Would you please change here how it should look like:
>>
>>> define = -DPOSRES
>>>
>>> integrator = md
>>> dt = 0.002
>>> emtol = 1000.0
>>> emstep = 0.01
>>> nsteps = 5000
>>>
>>> nstlist = 1
>>> rlist = 1.5
>>> rlistlong = 1.4
>>> rcoulomb = 1.5
>>> coulombtype = pme
>>> vdw-type = switch
>>> rvdw_switch = 0.8
>>> rvdw = 1.5
>>>
>>> nstxout = 100
>>> nstvout = 100
>>> nstenergy = 100
>>> nstlog = 100
>>>
>>> tcoupl = V-rescale
>>> tc-grps = ISO SOL
>>> tau_t = 0.1 0.1
>>> ref_t = 300 300
>>>
>>> pcoupl = no
>>
>> I am totaly frustrated and shortly for giving it up :-(:-( :-(
>>
>> Best greetings
>> Lara
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ----- Ursprüngliche Message -----
>> Von: Peter C. Lai <pcl at uab.edu>
>> An: Lara Bunte <lara.bunte at yahoo.de>
>> CC: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>> Gesendet: 17:57 Montag, 24.September 2012
>> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
>>
>> Then yes, your cutoffs are still wrong. However check to see if atom 8376 is
>> clashing with something nearby (protein?). You also never gave any data about
>> the result of the previous energy minimization steps...
>>
>> On 2012-09-24 04:54:13PM +0100, Lara Bunte wrote:
>>> Hi Peter
>>>
>>> My complete .mdp file is now:
>>>
>>> define = -DPOSRES
>>>
>>> integrator = md
>>> dt = 0.002
>>> emtol = 1000.0
>>> emstep = 0.01
>>> nsteps = 5000
>>>
>>> nstlist = 1
>>> rlist = 1.5
>>> rlistlong = 1.4
>>> rcoulomb = 1.5
>>> coulombtype = pme
>>> vdw-type = switch
>>> rvdw_switch = 0.8
>>> rvdw = 1.5
>>>
>>> nstxout = 100
>>> nstvout = 100
>>> nstenergy = 100
>>> nstlog = 100
>>>
>>> tcoupl = V-rescale
>>> tc-grps = ISO SOL
>>> tau_t = 0.1 0.1
>>> ref_t = 300 300
>>>
>>> pcoupl = no
>>>
>>> Greetings
>>> Lara
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ----- Ursprüngliche Message -----
>>> Von: Peter C. Lai <pcl at uab.edu>
>>> An: Lara Bunte <lara.bunte at yahoo.de>
>>> CC: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>>> Gesendet: 17:46 Montag, 24.September 2012
>>> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
>>>
>>> Is this energy minimization or actual integrator = md?
>>>
>>> On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote:
>>>> Hello
>>>>
>>>> Okay, I changed it to
>>>>
>>>> nstlist = 1
>>>> rlist = 1.5
>>>> rlistlong = 1.4
>>>> rcoulomb = 1.5
>>>> coulombtype = pme
>>>> vdw-type = switch
>>>> rvdw_switch = 0.8
>>>> rvdw = 1.5
>>>>
>>>> in my .mdp file and I got now this error:
>>>>
>>>> step 1352: Water molecule starting at atom 8376 can not be settled.
>>>> Check for bad contacts and/or reduce the timestep if appropriate.
>>>> Wrote pdb files with previous and current coordinates
>>>>
>>>> Are the .mdp Options still a problem?
>>>>
>>>>
>>>> I am really thankful for the big amount of help. Thank you.
>>>> Lara
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ----- Ursprüngliche Message -----
>>>> Von: Peter C. Lai <pcl at uab.edu>
>>>> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> CC: Lara Bunte <lara.bunte at yahoo.de>
>>>> Gesendet: 22:13 Freitag, 21.September 2012
>>>> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
>>>>
>>>> On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
>>>>>
>>>>>
>>>>> On 9/21/12 1:31 PM, Lara Bunte wrote:
>>>>>> Hi Justin
>>>>>>
>>>>>> I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with this settings grompp gives me two notes and one of this notes is inconsistent:
>>>>>>
>>>>>> NOTE 1 [file pr.mdp]:
>>>>>> For energy conservation with switch/shift potentials, rlist should be 0.1
>>>>>> to 0.3 nm larger than rvdw.
>>>>>>
>>>>>> Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my CHARMM27 force field.
>>>>>>
>>>>>>
>>>>>
>>>>> Increase rlist as suggested to accommodate the algorithm. Since CHARMM does not
>>>>> use charge groups (well, it uses single-atom charge groups) this isn't such a
>>>>> big deal. For a force field like Gromos96, it matters a lot more.
>>>>
>>>> Actually rlist has to be equal to rvdw for this case (PME will complain if it
>>>> doesn't). I haven't had a water settling issue in a correctly setup system
>>>> with rlist = rvdw and a switched rvdw. I do remember a bug in the code that
>>>> forgets rlistlong is specified.
>>>>
>>>>>
>>>>>>
>>>>>> My second note is:
>>>>>>
>>>>>> NOTE 2 [file pr.mdp]:
>>>>>> The sum of the two largest charge group radii (0.079505) is larger than
>>>>>> rlist (1.200000) - rvdw (1.200000)
>>>>>>
>>>>>>
>>>>>> which I sadly don't understand.
>>>>>>
>>>>>
>>>>> http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>>>>>
>>>>> -Justin
>>>>>
>>>>
>>>> I also get this note too, but the sum looks fine to me. If the sum > 0.15 then
>>>> it typically indicates chargegroups are being used, which they shouldn't for
>>>> charmm-based forcefields, but in this case the distance shown is on the order
>>>> of a heavy-h bond. I think the note message is still related to rlist vs.
>>>> rlistlong.
>>>>
>>>> anyway, I routinely ignore both these notes and it hasn't given me problems
>>>> so far. I would still go bck to check the specific water that could not settle
>>>> and see what the other particles near it are since that is probably the root
>>>> of the problem. Also, we haven't been told what the results of the energy
>>>> minimzation was...
>>>>
>>>> --
>>>> ==================================================================
>>>> Peter C. Lai | University of Alabama-Birmingham
>>>> Programmer/Analyst | KAUL 752A
>>>> Genetics, Div. of Research | 705 South 20th Street
>>>> pcl at uab.edu | Birmingham AL 35294-4461
>>>> (205) 690-0808 |
>>>> ==================================================================
>>>
>>> --
>>> ==================================================================
>>> Peter C. Lai | University of Alabama-Birmingham
>>> Programmer/Analyst | KAUL 752A
>>> Genetics, Div. of Research | 705 South 20th Street
>>> pcl at uab.edu | Birmingham AL 35294-4461
>>> (205) 690-0808 |
>>> ==================================================================
>>
>> --
>> ==================================================================
>> Peter C. Lai | University of Alabama-Birmingham
>> Programmer/Analyst | KAUL 752A
>> Genetics, Div. of Research | 705 South 20th Street
>> pcl at uab.edu | Birmingham AL 35294-4461
>> (205) 690-0808 |
>> ==================================================================
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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