[gmx-users] Re: cnt topology
Dr. Vitaly V. Chaban
vvchaban at gmail.com
Sat Dec 31 20:07:14 CET 2011
I hope you understand that I canNOT fix the problem by just looking
at several thousands on numbers in your topology... My preliminary
guess would be that the problem is localized in the dihedral section,
i.e. you don't define all the necessary dihedrals or define some of
them inconsistently with your GRO file.
I would start with visualizing you GRO including atom numbers and
checking manually if all the dihedrals you actually see are present in
the topology file. Usually, considering the very first circle of the
carbon atoms will give your an answer.
There is also a lazy solution. If you don't need a flexible tube, you
can just freeze its carbon atoms (in the MDP file), so that the
geomerty will be stable at all times
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
On Sat, Dec 31, 2011 at 1:42 PM, Zahra M <s_zahra_mousavi at yahoo.com> wrote:
> sorry I forget to attach my cnt topology file
>
> ________________________________
> From: Dr. Vitaly V. Chaban <vvchaban at gmail.com>
> To: Zahra M <s_zahra_mousavi at yahoo.com>
> Cc: gmx-users at gromacs.org
> Sent: Saturday, December 31, 2011 8:51 PM
> Subject: Re:
>
> Zahra:
>
> I believe the problem is in your topology (*.TOP) file which you don't
> attach. From your pictures, we see that the system does not survive
> energy minimization, so the intramolecular interactions are not
> simulated wisely.
>
> Happy New Year,
>
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> THE UNITED STATES OF AMERICA
>
>
>
> On Sat, Dec 31, 2011 at 11:58 AM, Zahra M <s_zahra_mousavi at yahoo.com> wrote:
>> Hi dear Dr. Vitaly
>> I'm simulating a system containing CNT and a protein with GROMACS, and I
>> encounter with some problems, as I understood (by reading articles) you've
>> worked on CNT simulation alot, so I decided to ask you for help. I wish
>> you
>> help me to solve my problem.
>> As I mentioned my system contains CNT and protein, in a dodecahedron unit
>> cell. when I run EM (although in vacuum) the shape of CNT changes, and its
>> bonds crash.
>> here are my MD parameters for EM:
>>
>> "
>> integrator = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol = 1000.0 ; Stop minimization when the maximum force <
>> 1000.0 kJ/mol/nm
>> emstep = 0.01 ; Energy step size
>> nsteps = 50000 ; Maximum number of (minimization) steps to
>> perform
>> nstlist = 1 ; Frequency to update the neighbor list and long
>> range forces
>> ns_type = grid ; Method to determine neighbor list (simple,
>> grid)
>> rlist = 1.0 ; Cut-off for making neighbor list (short range
>> forces)
>> domain-decomposition = no
>> coulombtype = PME ; Treatment of long range electrostatic
>> interactions
>> rcoulomb = 1.0 ; Short-range electrostatic cut-off
>> rvdw = 1.0 ; Short-range Van der Waals cut-off
>> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>> fourierspacing = 0.20
>> "
>>
>> but when I run mdrun command these lines appear in terminal:
>>
>> "
>> There were 16 inconsistent shifts. Check your topology
>>
>> ...
>> There were 16 inconsistent shifts. Check your topology
>> Warning: 1-4 interaction between 418 and 533 at distance 2.620 which is
>> larger than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> There were 16 inconsistent shifts. Check your topology 2.27716e+06, atom=
>> 536
>> Step= 1, Dmax= 1.0e-02 nm, Epot= 2.74550e+07 Fmax= 2.26527e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 2, Dmax= 1.2e-02 nm, Epot= 2.71314e+07 Fmax= 2.25101e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 3, Dmax= 1.4e-02 nm, Epot= 2.67459e+07 Fmax= 2.23390e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 4, Dmax= 1.7e-02 nm, Epot= 2.62873e+07 Fmax= 2.21339e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 5, Dmax= 2.1e-02 nm, Epot= 2.57427e+07 Fmax= 2.18879e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 6, Dmax= 2.5e-02 nm, Epot= 2.50973e+07 Fmax= 2.15928e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 7, Dmax= 3.0e-02 nm, Epot= 2.43348e+07 Fmax= 2.12391e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.34369e+07 Fmax= 2.08150e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.23854e+07 Fmax= 2.03066e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 10, Dmax= 5.2e-02 nm, Epot= 2.11653e+07 Fmax= 1.96974e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 11, Dmax= 6.2e-02 nm, Epot= 1.97571e+07 Fmax= 1.89657e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 12, Dmax= 7.4e-02 nm, Epot= 1.81605e+07 Fmax= 1.80954e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 13, Dmax= 8.9e-02 nm, Epot= 1.63847e+07 Fmax= 1.72347e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 14, Dmax= 1.1e-01 nm, Epot= 1.43324e+07 Fmax= 1.59766e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 15, Dmax= 1.3e-01 nm, Epot= 1.21562e+07 Fmax= 1.45696e+06, atom=
>> 536
>> There were 16 inconsistent shifts. Check your topology
>> Step= 16, Dmax= 1.5e-01 nm, Epot= 9.93679e+06 Fmax= 1.32228e+06, atom=
>> 545
>> There were 16 inconsistent shifts. Check your topology
>> Step= 17, Dmax= 1.8e-01 nm, Epot= 7.54598e+06 Fmax= 2.27192e+06, atom=
>> 526
>> There were 16 inconsistent shifts. Check your topology
>> Step= 18, Dmax= 2.2e-01 nm, Epot= 6.49375e+06 Fmax= 5.00565e+06, atom=
>> 530
>> There were 16 inconsistent shifts. Check your topology
>> There were 16 inconsistent shifts. Check your topology 3.04113e+11, atom=
>> 530
>> Step= 20, Dmax= 1.3e-01 nm, Epot= 6.13298e+06 Fmax= 9.98676e+05, atom=
>> 545
>> There were 2 inconsistent shifts. Check your topology
>> Step= 21, Dmax= 1.6e-01 nm, Epot= 4.72090e+06 Fmax= 1.06459e+06, atom=
>> 534
>> There were 2 inconsistent shifts. Check your topology
>> Step= 22, Dmax= 1.9e-01 nm, Epot= 3.74985e+06 Fmax= 7.47588e+05, atom=
>> 533
>> Step= 23, Dmax= 2.3e-01 nm, Epot= 2.46715e+06 Fmax= 2.56685e+06, atom=
>> 534
>> ...
>> Step= 406, Dmax= 9.8e-04 nm, Epot= 1.08559e+05 Fmax= 9.72907e+02, atom=
>> 532
>>
>> writing lowest energy coordinates.
>>
>> Back Off! I just backed up sys_vac_EM.gro to ./#sys_vac_EM.gro.1#
>>
>> Steepest Descents converged to Fmax < 1000 in 407 steps
>> Potential Energy = 1.0855916e+05
>> Maximum force = 9.7290698e+02 on atom 532
>> Norm of force = 1.5045358e+02
>> "
>>
>> As you see, my potential energy is positive. I'm confused, I read gmx user
>> list, but it doesn't help me, I hope you help me.
>> I attached the pictures of CNT while simulation.
>> Thank you in advance.
>> with best regards
>>
>> -Zahra
>>
>>
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