[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
Justin Lemkul
jalemkul at vt.edu
Fri Dec 7 20:24:26 CET 2012
On 12/7/12 2:21 PM, James Starlight wrote:
> Justin,
>
> with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
> rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
>
> NOTE 1 [file ./mdps/em.mdp]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
>
> NOTE 2 [file ./mdps/em.mdp]:
> The sum of the two largest charge group radii (0.078024) is larger than
> rlist (1.200000) - rvdw (1.200000)
>
As I recall, there is a small bug where grompp ignores rlistlong when printing
this message. The simulation will be fine.
-Justin
>
> Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
> value because of PME) ?
>
> 2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>> On 12/7/12 1:19 PM, James Starlight wrote:
>>> Justin,
>>>
>>> following to your advise I've tried to use charmm 27 ff for simulation
>>> of my protein-cGMP complex ( ligand was parametrized by Swiss Param
>>> server).
>>>
>>> Could you provide me with the cut-offs for vdw as well as
>>> electrostatics suitable for simulation in charmm27 and 36 force
>>> fields?
>>>
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
>>
>>> Does anybody know another servers for parametrization of the ligands
>>> for charmm simulation in gromacs?
>>>
>>
>> If Google can't find it, it probably doesn't exist.
>>
>> -Justin
>>
>>> 2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>
>>>> On 12/7/12 11:42 AM, James Starlight wrote:
>>>>> Justin,
>>>>>
>>>>> ligand-only simulation in vacuum have been finished with the same
>>>>> errors
>>>>> :)
>>>>>
>>>>> Step 19200, time 38.4 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.025443, max 0.140660 (between atoms 1 and 3)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 1 2 52.2 0.1033 0.0985 0.1000
>>>>> 1 3 90.1 0.1168 0.1141 0.1000
>>>>>
>>>>> Step 19200, time 38.4 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.025376, max 0.140474 (between atoms 1 and 3)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 1 2 52.0 0.1033 0.0988 0.1000
>>>>> 1 3 90.0 0.1168 0.1140 0.1000
>>>>> step 19200, will finish Sat Dec 8 04:10:49 2012
>>>>> Step 19201, time 38.402 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.052715, max 0.293316 (between atoms 1 and 3)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 1 2 49.3 0.0988 0.0993 0.1000
>>>>> 1 3 90.0 0.1140 0.1293 0.1000
>>>>>
>>>>> Step 19201, time 38.402 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.052900, max 0.294281 (between atoms 1 and 3)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 1 2 49.6 0.0988 0.0989 0.1000
>>>>> 1 3 90.0 0.1140 0.1294 0.1000
>>>>>
>>>>> Step 19202, time 38.404 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.035783, max 0.198482 (between atoms 1 and 3)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 1 2 33.3 0.0989 0.0984 0.1000
>>>>> 1 3 89.9 0.1294 0.1198 0.1000
>>>>>
>>>>> -------------------------------------------------------
>>>>> Program mdrun, VERSION 4.5.4
>>>>> Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176
>>>>>
>>>>> Fatal error:
>>>>> Too many LINCS warnings (1000)
>>>>>
>>>>>
>>>>> ITs intresting that the same files (like step-1c_n11.pdb) have been
>>>>> produced already during CG minimisation phase but the system have not
>>>>> been crashed. So I suppoe that the problem is in geometry of the
>>>>
>>>> If you get errors in the minimization, that should indicate that either
>>>> the
>>>>
>>>> topology or configuration is flawed.
>>>>
>>>>> mollecule. The direct comparison of the bonds and angles with the rtp
>>>>> (DGUA) is non trivial again because of differs in the file formats
>>>>> representation :)
>>>>>
>>>>
>>>> Most troubleshooting is not easy. You can also create a topology for
>>>> DGUA
>>>> from
>>>> just about any DNA structure and compare its .top against your cGMP
>>>> topology.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> --
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>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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--
========================================
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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