Yes, it executes. With nstlim=1 it ends correctly. With sander.MPI the
> 3. ATOMIC COORDINATES AND VELOCITIES
part is exactly the same (same warnings) as with pmemd. Therefore, I
started a long procedure with pmemd. No problem for me with new/old,
with pmemd it is as if there were more processors. The only problem is
bothering experts when it does not execute or messages are cryptic.
Thanks
francesco
On Mon, Nov 17, 2008 at 8:58 PM, Robert Duke <rduke.email.unc.edu> wrote:
> And it executes, right? Positional restraints are different than nmr
> restraints; nmr restraints have to be defined with redirection files, and
> you are not using them here; the code is just reporting that there are none,
> since you are using nmropt .eq. 1 (which is required to use redirection
> file-based nmr restraints). So you SHOULD be okay, I think (but am not
> certain since I have not seen all your output). This stuff is convoluted
> due to a lot of history; folks have been able to get pmemd to do what they
> want, but I think there were some restrictions on how you specified the nmr
> restraints. Since I never use nmr restraints, I am a little vague in this
> area. We should probably move to a newer more sane mdin format, but then a
> lot of old stuff wouldn't work. In s/w, you can have to live with old
> decisions for a very long time...
> Best Regards - Bob
>
> ----- Original Message ----- From: "Francesco Pietra"
> <chiendarret.gmail.com>
> To: <amber.scripps.edu>
> Sent: Monday, November 17, 2008 2:21 PM
> Subject: Re: AMBER: RESTRAINTS: no valid redirection found
>
>
>> I added the lacking flag, now the line for restraint in the in file reads
>>
>> nmropt=1, ntr=1,
>>
>>
>> Now the positional restraints are read correctly. However, the out
>> file warns that:
>>
>> 3. ATOMIC COORDINATES AND VELOCITIES
>>
>> --------------------------------------------------------------------------------
>>
>>
>> begin time read from input coords = 10.000 ps
>>
>>
>>
>> Begin reading energy term weight changes/NMR restraints
>> WEIGHT CHANGES:
>> TEMP0 0 600 290.000000 300.000000 0 0
>>
>> RESTRAINTS:
>> No valid redirection requests found
>> ** No restraint defined **
>>
>> Done reading weight changes/NMR restraints
>>
>>
>> Number of triangulated 3-point waters found: 0
>> | Dynamic Memory, Types Used:
>> | Reals 771203
>> | Integers 1594280
>>
>>
>> If the flag "nmropt=1" is removed, that warning "No valid request .."
>> disappears, but the weight restraint on the temperature is not read.
>>
>> Does this simply mean that there are nothing else to do about
>> "nmropt=1" (and the warning should be ignored) or is the procedure
>> wrongly started?
>>
>> pmemd is used with mpirun
>>
>> Thanks
>> francesco
>>
>>
>>
>>
>>
>> On Mon, Nov 17, 2008 at 6:34 PM, Robert Duke <rduke.email.unc.edu> wrote:
>>>
>>> I don't see an ntr=1 in the &cntrl. - Bob Duke
>>> ----- Original Message ----- From: "Francesco Pietra"
>>> <chiendarret.gmail.com>
>>> To: "Amber" <amber.scripps.edu>
>>> Sent: Monday, November 17, 2008 12:15 PM
>>> Subject: AMBER: RESTRAINTS: no valid redirection found
>>>
>>>
>>>> With pmemd (i.e., I can't use restraintmask) in Amber10 the following
>>>> heat5.in file
>>>>
>>>> Heating gradually under GB conditions
>>>> with restraint on Cl-
>>>> Then continuing equilibration at 300K.
>>>> &cntrl
>>>> imin=0, irest=0, ntx=1, ntb=0,
>>>> igb=5, ntc=2, ntf=2,
>>>> ntt=3, gamma_ln=2.0,
>>>> nstlim=3000, dt=0.002,
>>>> ntpr=100, ntwx=100,
>>>> tempi=290.0, temp0=300.0,
>>>> cut=999.0, rgbmax=999.0,
>>>> nmropt=1
>>>> /
>>>> &wt TYPE='TEMP0', istep1=0, istep2=600,
>>>> value1=290.0, value2=300.0,
>>>> /
>>>> &wt TYPE='END'
>>>> /
>>>> Keep Cl- 427 restrained
>>>> 32.0
>>>> RES 427
>>>> END
>>>> END
>>>>
>>>> (actually there are several other C-, same layout)
>>>>
>>>> did not succeed in imposing positional restraints, as from the out file:
>>>>
>>>> begin time read from input coords = 10.000 ps
>>>>
>>>>
>>>>
>>>> Begin reading energy term weight changes/NMR restraints
>>>> WEIGHT CHANGES:
>>>> TEMP0 0 600 290.000000 300.000000 0 0
>>>>
>>>> RESTRAINTS:
>>>> No valid redirection requests found
>>>> ** No restraint defined **
>>>>
>>>> Done reading weight changes/NMR restraints
>>>>
>>>>
>>>> In previous procedure heat4.in (from which heat4.rst was used to
>>>> launch this procedure) there was no positional restraint. Does ""No
>>>> valid redirection" mean that positional restraint should be placed
>>>> before weigth restraint?
>>>>
>>>> Thanks
>>>>
>>>> francesco pietra
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Received on Fri Dec 05 2008 - 15:47:25 PST
