I'm not sure about later steps, but your heating input has errors. You set
nstlim=1000, but then for the thermostat changes you have this:
&wt type='TEMP0',istep1=0,
istep2=500, value1=100.0,value2=300.0,
&end
&wt type='TEMP0',istep1=5001,
istep2=10000, value1=300.0,value2=300.0,
&end
&wt type='END', &end
notice that you heat very quickly (500 MD steps) to 300K, and then define
it again for step 5001 and on, which does not exist in this simulation.
if you look at the mdout file, you can see that at step 500 it has not yet
reached 300K. This may be from using ntt=1, which is not the thermostat
that people normally use (I think ntt=3 is much more common). You could
also modify the coupling constant (tautp), but I think you're better off
using ntt=3. The temperature continues to slowly rise, but has not reached
your target at the end, so you should not continue to the next step yet.
overall you are using a relatively simple relaxation protocol. I suggest
looking at the Amber web page tutorials to see something that is more
modern. it isn't for RNA, but you should be able to adapt the general ideas.
https://ambermd.org/tutorials/basic/tutorial13/index.php
On Wed, Feb 8, 2023 at 10:47 AM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Thank you, Prof. Simmerling for your helpful response. I apologize for
> sending the wrong output files. Indeed, it does look like I was able to
> solve the issue of low density by modifying how I built the waterbox
> following your suggestion in an earlier email.
>
> However, I notice now that there is a new issue. In the equilibration
> stage, there is an intermittent error of exceeding 'vlimit' as below:
>
> eq.mdout: t = 0.00000, dt = 0.00200, vlimit = 20.00000
> eq.mdout:vlimit exceeded for step 67130; vmax = 41.0592
> eq.mdout:vlimit exceeded for step 67131; vmax = 31.1308
> eq.mdout:vlimit exceeded for step 67132; vmax = 29.9301
> eq.mdout:vlimit exceeded for step 67133; vmax = 20.7105
> eq.mdout:vlimit exceeded for step 67135; vmax = 26.6603
> eq.mdout:vlimit exceeded for step 67136; vmax = 38.0706
> eq.mdout:vlimit exceeded for step 67145; vmax = 21.1061
> eq.mdout:vlimit exceeded for step 67206; vmax = 21.1132
> eq.mdout:vlimit exceeded for step 67217; vmax = 20.3974
> eq.mdout:vlimit exceeded for step 67276; vmax = 22.7971
> eq.mdout:vlimit exceeded for step 67298; vmax = 21.0155
> eq.mdout:vlimit exceeded for step 67302; vmax = 20.4616
> eq.mdout:vlimit exceeded for step 67324; vmax = 20.8580
> eq.mdout:vlimit exceeded for step 110108; vmax = 35.5854
> eq.mdout:vlimit exceeded for step 110109; vmax = 22.3098
> eq.mdout:vlimit exceeded for step 110110; vmax = 23.9470
> eq.mdout:vlimit exceeded for step 110113; vmax = 21.0085
> eq.mdout:vlimit exceeded for step 110114; vmax = 21.2495
> eq.mdout:vlimit exceeded for step 110116; vmax = 21.5208
> eq.mdout:vlimit exceeded for step 110124; vmax = 221.6161
> eq.mdout:vlimit exceeded for step 110125; vmax = 25.9272
> eq.mdout:vlimit exceeded for step 110126; vmax = 20.7325
> eq.mdout:vlimit exceeded for step 110127; vmax = 24.5213
> eq.mdout:vlimit exceeded for step 110129; vmax = 21.0525
> eq.mdout:vlimit exceeded for step 110131; vmax = 23.6221
> eq.mdout:vlimit exceeded for step 110133; vmax = 28.7984
>
> I do not see this error in the heating stage. However, the subsequent
> production run crashes. I attached the input files I used and the
> corresponding output files. In the md_1.mdout file, after a certain number
> of steps (at TIME = 237.54 ps), I notice that TEMP(K) = NaN, and PRESS =
> ******
> What is odd is that the value of PRESS as it is printed out fluctuates
> between positive and negative values. Does this indicate a problem with any
> input file parameter?
>
> Thank you for your time and continued help.
>
> Sincerely,
> PN
>
> eq.mdout
> <https://drive.google.com/file/d/10GDaOG7N-iSBTinwoOvQLdHF-4k7K2ce/view?usp=drive_web>
> heat.mdout
> <https://drive.google.com/file/d/1A9HrHr2vxWz9lI5Y6QHQbTM6GOdQia-S/view?usp=drive_web>
> md_1.mdout
> <https://drive.google.com/file/d/1RrbCeCc9nq9MvpPRaD6okvP_olOGAloK/view?usp=drive_web>
> mini.mdout
> <https://drive.google.com/file/d/1xEdo65b_kSH6J3Ielmr5hNIlR4g1NF9H/view?usp=drive_web>
>
>
>
> On Wed, Feb 8, 2023 at 7:21 AM Carlos Simmerling via AMBER <
> amber.ambermd.org> wrote:
>
>> the "step4.1_equilibration" output here doesn't match what you sent
>> before.
>> this one goes to a density of 1 rather quickly, which Prof Case mentioned
>> was a problem in the previous one. Maybe you need to send updated
>> information about the problem observed with these specific outputs - I
>> didn't see any error in the files that you attached.
>>
>> On Tue, Feb 7, 2023 at 10:37 AM Prithviraj Nandigrami <
>> prithviraj.nandigrami.gmail.com> wrote:
>>
>> > Thank you, Dr. Case and Dr. Simmerling for your helpful suggestions. The
>> > input pdb file was processed through 'pdb4amber' prior to system
>> > preparation using tleap.
>> >
>> > Here are the commands I used to prepare and solvate the system in tleap:
>> >
>> > parm10 = loadamberparams parm10.dat
>> > loadOff terminal_monophosphate.lib
>> > source leaprc.water.tip3p
>> > loadAmberParams frcmod.tip3p
>> > loadamberparams M6A.frcmod
>> > M6A = loadMol2 M6A.mol2
>> > addions mol Na+ 0
>> > solvateOct mol TIP3PBOX 12.0 0.75
>> > saveAmberParm mol 2L1F.GAACA.M6A.parm7 2L1F.GAACA.M6A.rst7
>> >
>> > I also attached the pdb4amber output file (before tleap) and the output
>> > prepared system after tleap, as well as the output log file for tleap.
>> > Also, attached is the AMBER minimization and equilibration log files.
>> >
>> > I would appreciate any help regarding this.
>> >
>> > Sincerely,
>> > PN
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Tue, Feb 7, 2023 at 8:26 AM David A Case <david.case.rutgers.edu>
>> > wrote:
>> >
>> >> On Mon, Feb 06, 2023, Prithviraj Nandigrami via AMBER wrote:
>> >> >This is what the density looks like in the mdout files:
>> >> >
>> >> >*Equilibration *
>> >> >
>> >> > 0.8121
>> >> > 0.7651
>> >> > 0.7322
>> >> > 0.7139
>> >> > 0.7063
>> >> ....
>> >> >*Production*
>> >> >
>> >> > 0.7694
>> >> > 0.7699
>> >> > 0.7722
>> >> > 0.7744
>> >> > 0.7767
>> >>
>> >> ...
>> >>
>> >> These are *very* low densities, certainly for a simulation of a
>> >> macromolecule in water. The fact that they don't quickly approach a
>> value
>> >> near 1.0 (since most of a typical system is water) suggests some
>> problem
>> >> with the setup of the system. I don't have enough info now to grok
>> >> what the most likely problem is there.
>> >>
>> >> ....dac
>> >>
>> >>
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>>
>
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Received on Wed Feb 08 2023 - 08:30:02 PST
