Do you see energies being printed every 500 steps in the .out file?
Bill
On 6/28/17 12:47 PM, Sumudu Leelananda wrote:
> This is Step2_min0.in
>
> I will try without mpi as well. Thank you.
>
> System minimization:
> &cntrl
> imin=1, ntmin=2, nmropt=0, drms=0.1
> maxcyc=20000, ncyc=1500,
> ntx=1, irest=0,
> ntpr=500, ntwr=500, ntwx=500, iwrap=1,
> ntf=1, ntb=1, cut=10.0, nsnb=20,
> ntc=1,
> icfe = 1, ifsc = 0,
> clambda=0.5,
> ioutfm=1,
> nmropt=1/
> &wt type='DUMPFREQ', istep1=500, /
> &wt type='END', /
> DISANG=rest_step2.in
> DUMPAVE=rest.txt
> LISTIN=POUT
> LISTOUT=POUT /
> &end
>
>
>
> On Wed, Jun 28, 2017 at 3:43 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Please paste step2_min0.in here.
>>
>> Also, you might try without mpi.
>>
>> Bill
>>
>>
>> On 6/28/17 12:29 PM, Sumudu Leelananda wrote:
>>> I could not find any errors in that out file... Any hints?
>>>
>>> Thank you!
>>>
>>> On Wed, Jun 28, 2017 at 3:08 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>
>>>> Look at step2_min0.out for clues as to why the rst wasn't generated.
>>>>
>>>> Bill
>>>>
>>>>
>>>> On 6/28/17 12:05 PM, Sumudu Leelananda wrote:
>>>>> Dear Dr. Loeffler
>>>>>
>>>>> Thank you for your suggestion. I tried it but it still gives the same
>>>> error:
>>>>> Error opening unit 30: File "step2_min0.rst" is missing or unreadable
>>>>>
>>>>> I attached the inputs and also the output files for the charge step.
>>>>>
>>>>> mpiexec sander.MPI -O -i step2_min0.in -o step2_min0.out -c
>>>>> protein_1CA6.inpcrd -p protein_1CA6.prmtop -r step2_min0.rst -ref
>>>>> protein_1CA6.inpcrd
>>>>>
>>>>> mpiexec sander.MPI -O -i step2_min1.in -o step2_min1.out -c
>>>>> protein_1CA6.inpcrd -p protein_1CA6.prmtop -r step2_min1.rst -ref
>>>>> protein_1CA6.inpcrd
>>>>>
>>>>> mpiexec sander.MPI -O -i step2_heat0.in -o step2_heat0.out -c
>>>>> step2_min0.rst -p protein_1CA6.prmtop -r step2_heat0.rst -x
>>>> step2_heat0.nc
>>>>> -ref step2_min0.rst
>>>>>
>>>>> mpiexec sander.MPI -O -i step2_heat1.in -o step2_heat1.out -c
>>>>> step2_min1.rst -p protein_1CA6.prmtop -r step2_heat1.rst -x
>>>> step2_heat1.nc
>>>>> -ref step2_min1.rst
>>>>>
>>>>> mpiexec sander.MPI -O -i step2_md0.in -o step2_md0.out -c
>>>> step2_heat0.rst
>>>>> -p protein_1CA6.prmtop -r step2_md0.rst -x step2_md0.nc -ref
>>>> step2_heat0.rst
>>>>> mpiexec sander.MPI -O -i step2_md1.in -o step2_md1.out -c
>>>> step2_heat1.rst
>>>>> -p protein_1CA6.prmtop -r step2_md1.rst -x step2_md1.nc -ref
>>>> step2_heat1.rst
>>>>> Could you please give me suggestions or hints on this?
>>>>>
>>>>> Also, according to what you suggested it seems like we don't need a
>>>>> restraint step when doing Sander? I can just only have the charge
>> removal
>>>>> step [2] and the van der Waals forces removal step [3]. Is that right?
>>>>>
>>>>> Thank you!
>>>>>
>>>>> On Wed, Jun 28, 2017 at 12:18 PM, Sumudu Leelananda <
>>>>> sumudu.leelananda.gmail.com> wrote:
>>>>>
>>>>>> Dear Dr. Loeffler
>>>>>>
>>>>>> Thank you for your suggestion. I tried it but it still gives the same
>>>>>> error:
>>>>>>
>>>>>> Error opening unit 30: File "step2_min0.rst" is missing or
>> unreadable
>>>>>> I attached the inputs and also the output files for the charge step.
>>>>>>
>>>>>> Could you please give me suggestions on this?
>>>>>>
>>>>>> Also, according to what you suggested it seems like we don't need a
>>>>>> restraint step when doing Sander? I can just only have the charge
>>>> removal
>>>>>> step [2] and the van der Waals forces removal step [3]. Is that right?
>>>>>>
>>>>>> Thank you!
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 2, 2017 at 3:19 AM, Hannes Loeffler <
>>>>>> Hannes.Loeffler.stfc.ac.uk> wrote:
>>>>>>
>>>>>>> On Thu, 1 Jun 2017 15:22:53 -0400
>>>>>>> Sumudu Leelananda <sumudu.leelananda.gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear Hannes
>>>>>>>>
>>>>>>>> Thank you for your reply. I'm sorry, I only got a part of your
>> reply
>>>>>>>> and don't see the full reply on the archives yet. Yes. I'm using a
>>>>>>>> similar multisite Calcium model but the number of dummy atoms is
>>>>>>>> different than Sept Model you provided the link to.
>>>>>>>>
>>>>>>>> In PEMED I had 2 Ca ions in the restraint step (residue numbers 90
>>>>>>>> and 91). What I do is restraint 90 at the end of the restraint step.
>>>>>>>> Then in the charge step remove the charge from 91 and in the vdW
>> step
>>>>>>>> totally remove 91. PEMED calculations worked without any issues.
>>>>>>>> Issues arise for Sander.
>>>>>>> So step 2 would be
>>>>>>> icfe = 1, ifsc = 0,
>>>>>>> timask1 = ':90', timask2 = ':91',
>>>>>>> crgmask = ':91'
>>>>>>>
>>>>>>> And step 3
>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
>>>>>>> timask1 = ':90', timask2 = '',
>>>>>>> scmask1 = ':90', scmask2 = ''
>>>>>>> crgmask = ':90'
>>>>>>>
>>>>>>> Step 3 obviously implies that you don't have a residue 91.
>>>>>>>
>>>>>>>
>>>>>>>> In Sander which I'm doing now, I didn't see the need to have two
>>>>>>>> copies like that so I only have 90.
>>>>>>> Sander needs two topology files and two input files, and it doesn't
>>>> have
>>>>>>> timask.
>>>>>>>
>>>>>>> So 2a:
>>>>>>> icfe = 1, ifsc = 0,
>>>>>>>
>>>>>>> and 2b
>>>>>>> icfe = 1, ifsc = 0,
>>>>>>> crgmask = ':90'
>>>>>>>
>>>>>>>
>>>>>>> 3a:
>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
>>>>>>> scmask = ':90'
>>>>>>> crgmask = ':90'
>>>>>>>
>>>>>>> 3b:
>>>>>>> icfe = 1, ifsc = 1, scalpha = 0.5,
>>>>>>> scmask = ''
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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Received on Wed Jun 28 2017 - 13:00:04 PDT
