I suggest running without the ligand and checking that.
On May 18, 2010, at 10:17 AM, Senthil Natesan <sen.natesan.yahoo.com>
wrote:
>
>
> Dr. Simmerling,
>
> Thanks. Yes I posted volume and density plots ( I am attaching here
> again) and people suggested that they
> don't see proper convergence (I wrote the output every 500 steps, I
> guess that is the reason for spikes)
> So I am running long simulations now with suggested parameters. As
> far as force field parameters, I am using standard Amber force
> fieldleaprc.ff02. For ligands, I used GAFF and there is no warning
> in the frcmod file.
> I will report here again once I finish the simulations.
>
> Senthil
>
>
>
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Mon, May 17, 2010 10:41:59 PM
> Subject: Re: [AMBER] solvent MD - poor equilibration
>
> first, plot volume and density vs time and see the profile. you can't
> check equilibration with a single snapshot.
> for force field, please tell us if the simulation is all standard
> Amber parameters, or if you created anything new.
>
>
> On Mon, May 17, 2010 at 3:12 PM, Senthil Natesan <sen.natesan.yahoo.com
> > wrote:
>> Thanks Bill, Paul and Carlos for your valuable suggestions. Now I
>> ran 40 ps constant pressure
>> simulation with taup = 0.1 (after 20 ps constant volume run). I
>> reimaged the .rst file and here is the output.
>> Please look at the snapshot of the complex and the arrow-pointed
>> region. I am attaching all analysis
>> pictures.
>>
>> Dr. Simmerling suggested me to check whether there is any bad force
>> field parameters? can anyone
>> educate me how to do the same?
>>
>>
>>
>> ---
>> ---
>> ---
>> ---------------------------------------------------------------------
>> A V E R A G E S O V E R 80 S T E P S
>>
>> NSTEP = 40000 TIME(PS) = 60.000 TEMP
>> (K) = 300.32 PRESS = 1.6
>> Etot = -44706.7284 EKtot = 20935.9646
>> EPtot = -65642.6930
>> BOND = 13187.8322 ANGLE = 2153.6667
>> DIHED = 3131.7413
>> 1-4 NB = 998.3376 1-4 EEL = 13428.8920
>> VDWAALS = 9418.6629
>> EELEC = -109086.9867 EHBOND = 0.0000
>> RESTRAINT = 1125.1611
>> EAMBER (non-restraint) = -66767.8541
>> EKCMT = 5617.2295 VIRIAL = 5608.3618 VOLUME = 256293.1378
>> Density
>> = 0.9430
>> Ewald error estimate: 0.5938E-04
>> ---
>> ---
>> ---
>> ---------------------------------------------------------------------
>>
>> R M S F L U C T U A T I O N S
>>
>> NSTEP = 40000 TIME(PS) = 60.000 TEMP(K) = 1.61
>> PRESS = 93.2
>> Etot = 238.6872 EKtot = 112.4630 EPtot
>> = 196.7113
>> BOND = 114.6308 ANGLE = 38.0862 DIHED
>> = 15.4679
>> 1-4 NB = 11.4936 1-4 EEL = 25.6773 VDWAALS
>> = 144.6216
>> EELEC = 267.1154 EHBOND = 0.0000 RESTRAINT
>> = 47.2495
>> EAMBER (non-restraint) = 149.4617
>> EKCMT = 60.0166 VIRIAL = 522.8410 VOLUME
>> = 2129.6454
>> Density
>> = 0.0077
>> Ewald error estimate: 0.3859E-04
>> ---
>> ---
>> ---
>> ---------------------------------------------------------------------
>> thanks so much..
>>
>> Senthil
>>
>>
>>
>>
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>>
>>
>
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> <volume.png>
> <density.png>
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Received on Tue May 18 2010 - 08:30:03 PDT
