Hey King Wu,
I’ve been struggling my fair share aswell on lipids,
However for this particular error
‘
rfree: Error decoding variable 4 2 from:
ATOM 1 34438 !
‘
I think you should erase the tekst,
So just:
Hold lipid fixed
10.0
RES 1 384
END
END
Vic De Roo
PhD Student
NMRSTR Group<
https://www.ugent.be/we/orgchem/nmr-structure-analysis/en>
Department of Organic and Macromolecular Chemistry
Krijgslaan 281, S4-bis, 1st floor
B-9000 GENT
Belgium
+32456123894
Van: King Wu<mailto:lodking407.gmail.com>
Verzonden: dinsdag 15 februari 2022 23:02
Aan: AMBER Mailing List<mailto:amber.ambermd.org>
Onderwerp: Re: [AMBER] MD simulations for POPC membrane
Hi, Amber,
I followed the AMBER tutorial heat.in with the following setup, but got an
error message in the output file. I also tried the "RES" flag with 1 771 in
the GROUP and got the same error (because my POPC residues are from 1 to
771, or atoms are from 1 to 34438).
Can somebody tell me how to fix this? The tutorial has RES 1 384, but the
DOPC_128.pdb has 128 lipids, so I am not sure why here it is set to 1 384.
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
Hold lipid fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
rfree: Error decoding variable 4 2 from:
ATOM 1 34438 !
Lipid POPC heating 100K
&cntrl
imin=0, ! Molecular dynamics
ntx=1, ! Positions read formatted with no initial velocities
irest=0, ! No restart
ntc=2, ! SHAKE on for bonds with hydrogen
ntf=2, ! No force evaluation for bonds with hydrogen
tol=0.0000001, ! SHAKE tolerance
nstlim=2500, ! Number of MD steps
ntt=3, ! Langevin thermostat
gamma_ln=1.0, ! Collision frequency for Langevin thermostat
ntr=1, ! Restrain atoms using a harmonic potential
! (See the GROUP input below)
ig=-1, ! Random seed for Langevin thermostat
ntpr=100,
ntwr=10000,
ntwx=100, ! Write to trajectory file every ntwx steps
dt=0.002, ! Timestep (ps)
nmropt=1, ! NMR restraints will be read (See TEMP0 control below)
ntb=1,
ntp=0,
cut=12.0,
ioutfm=1, ! Write a binary (netcdf) trajectory
ntxo=2, ! Write binary restart files
/
&wt
type='TEMP0', ! Varies the target temperature TEMP0
istep1=0, ! Initial step
istep2=2500, ! Final step
value1=0.0, ! Initial temp0 (K)
value2=100.0 / ! final temp0 (K)
&wt type='END' / ! End of varying conditions
Hold lipid fixed
10.0 ! Force constant (kcal/(mol Angstroms^2))
ATOM 1 34438 ! Choose residues
END
END ! End GROUP input
My run script is : $AMBERHOME/bin/pmemd.cuda -O -i heat01.in -o heat01.out
-p protein_popc_water.prmtop -c min_all.rst -r heat01.rst -x heat01.mdcrd
-ref min_all.rst
On Tue, Feb 15, 2022 at 9:41 AM King Wu <lodking407.gmail.com> wrote:
> Yes, I did.
>
> I compared my input and this tutorial's input, I did not find any
> restraint flags for the production run. Therefore I went ahead to run my
> 100ns simulation.
>
> But I noticed that there is "RES" in the Heat up steps, and one step to
> Hold. Is the Hold step a necessary step before production runs?
>
> and thank you, Elvis, for the input. Tutorial uses ntp=2, I will use ntp=3
> to give a try, and at the same time, I will try the "RES" flags in the
> heat.in and then "hold.in" step.
>
> On Tue, Feb 15, 2022 at 9:23 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> have you looked at the lipid tutorial?
>> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial16%2Findex.php&data=04%7C01%7CVic.DeRoo%40ugent.be%7C49a65fe57d074e6b93a808d9f0cedd98%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637805593545438265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=2epO%2BgDOdTc4Z%2FgjN4YMrNOtg7GRDbWj8%2FUCa2au%2BcQ%3D&reserved=0
>>
>> On Tue, Feb 15, 2022 at 11:38 AM King Wu <lodking407.gmail.com> wrote:
>>
>> > My simulation system includes a protein and a membrane. I want to
>> > investigate the dynamics of the protein with the presence of a membrane.
>> >
>> > I used FF14SB for the protein and LIPID17 for the membrane. During the
>> > equilibrium step, I first restrained the solute and simulated the water
>> at
>> > 300K, then I heated up the whole system from low T to reach the RT
>> without
>> > restraint. Appropriate Na and Cl ions were added to neutralize the
>> system.
>> >
>> > The equ and production MD runs are in the explicit solvent model.
>> >
>> > Please let me know if additional info is needed. I would be happy to
>> > provide.
>> >
>> > Thanks.
>> >
>> > On Tue, Feb 15, 2022 at 8:26 AM Carlos Simmerling <
>> > carlos.simmerling.gmail.com> wrote:
>> >
>> > > I think people might be able to offer help if you give a lot more
>> > > information on exactly what you did, and what happened. For example,
>> you
>> > > don't say what force field you used for the lipid, or how you
>> > equilibrated
>> > > it, or if water was included, and so on.
>> > >
>> > > On Tue, Feb 15, 2022 at 11:21 AM King Wu <lodking407.gmail.com>
>> wrote:
>> > >
>> > > > Hi, Amber,
>> > > >
>> > > > I wonder if you received my previous email.
>> > > >
>> > > > I simulated a 100 ns simulation for a VMD generated POPC membrane. I
>> > > > started with 120 X 80 A dimension, but got an aggregated/folded
>> > > > conformation of the membrane after 100ns simulation. Do I miss any
>> > flags
>> > > > of restrain in the input for my production run?
>> > > > Because the screenshots are large in size, I could not attach them
>> for
>> > > your
>> > > > reference.
>> > > > Below is the input:
>> > > >
>> > > > &cntrl
>> > > > imin = 0,
>> > > > irest = 1,
>> > > > ntx = 5,
>> > > > ioutfm = 1,
>> > > > nstlim = 10000000,
>> > > > dt = 0.002,
>> > > > ntt = 3,
>> > > > gamma_ln = 2.0,
>> > > > ig = -1,
>> > > > tempi = 300.0,
>> > > > temp0 = 300.0,
>> > > > ntp = 1,
>> > > > ntb = 2,
>> > > > ntc = 2,
>> > > > ntf = 2,
>> > > > cut = 12,
>> > > > ntwr = 500,
>> > > > ntpr = 500,
>> > > > ntwx = 500,
>> > > > ntwe = 500,
>> > > > iwrap = 1,
>> > > > ntr = 0,
>> > > > /
>> > > > $ewald
>> > > >
>> > > >
>> > > > /
>> > > > _______________________________________________
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Received on Tue Feb 15 2022 - 16:30:02 PST
