I use pmemd.MPI. I got the following error.
set AMBER=/home/srabani/Downloads/amber18/bin/pmemd.MPI
finddgref.py -do_parallel mpirun -np 6 -mdexec
/home/srabani/Downloads/amber18/bin/pmemd.MPI -ng 6 -groupfile groupfile001
-target 6.6 -bin-path /home/srabani/Downloads/amber18/bin
Checking cpin file and/or cein file.
We are going to find DELTAGREF for a pH titratable residue using Replica
Exchange.
The solvent pH value of replica 1 is 6.200 and was loaded from the
mdin file (001/001.in).
The solvent pH value of replica 2 is 6.400 and was loaded from the
mdin file (002/002.in).
The solvent pH value of replica 3 is 6.600 and was loaded from the
mdin file (003/003.in).
The solvent pH value of replica 4 is 6.800 and was loaded from the
mdin file (004/004.in).
The solvent pH value of replica 5 is 7.000 and was loaded from the
mdin file (005/005.in).
The solvent pH value of replica 6 is 7.200 and was loaded from the
mdin file (006/006.in).
The target pKa is 6.60000.
The temperature is 300.00 K and was loaded from the mdin file (001/001.in
).
According to the mdin file (001/001.in), the value of ntcnstph is 500.
According to the mdin file (001/001.in), the value of nstlim is 2000.
According to the mdin file (001/001.in), the value of numexchg is 10000.
The program will try to find a range of values for DELTAGREF
automatically, as the argument -dgrefrange was not given
AMBER execution #1: running 10000000 MD steps (5000 replica exchange
attempts) for DELTAGREF = 0.000000 kcal/mol
ERROR: The execution of AMBER using the binary
/home/srabani/Downloads/amber18/bin/pmemd.MPI failed. The execution
returned the following STDERR:
setup_groups: MPI size is not a multiple of -ng
The command executed was:
mpirun -np 6 /home/srabani/Downloads/amber18/bin/pmemd.MPI -ng 6
-groupfile groupfile001.temporary
Check the mdout file (001/mdout.rep.001) to see what the error might
be. Also check if all libraries necessary to run AMBER are properly set.
The execution of finddgref.py stopped
unset echo
There is no generation of mdout file.
On Tue, Jun 11, 2024 at 10:44 AM Vinicius Cruzeiro <
vcruzeiro.architecttherapeutics.com> wrote:
> Ok. I suggest you try to use pmemd.MPI instead of pmemd.cuda.MPI just to
> see if any error messages pop up.
>
> Best,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Scientist II, Computational Chemistry
> Architect Therapeutics
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> *Sent:* Monday, June 10, 2024 10:11 PM
> *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>; AMBER
> Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] finddgref.py using pH-REMD
>
> Respected sir,
> Thank you for your response. I check all six mdout files. All are the same.
>
> On Tue, Jun 11, 2024 at 10:33 AM Vinicius Cruzeiro <
> vcruzeiro.architecttherapeutics.com> wrote:
>
> Did you check all your MDOUT files?
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Scientist II, Computational Chemistry
> Architect Therapeutics
> Twitter: @vwcruzeiro
> ------------------------------
> *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> *Sent:* Monday, June 10, 2024 7:45 PM
> *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>
> *Subject:* Re: [AMBER] finddgref.py using pH-REMD
>
> No, I do not see any error messages. my out file is like below.
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 39.455 Box Y = 38.946 Box Z = 35.199
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 40 NFFT2 = 40 NFFT3 = 36
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
> | PMEMD ewald parallel performance parameters:
> | block_fft = 0
> | fft_blk_y_divisor = 2
> | excl_recip = 0
> | excl_master = 0
> | atm_redist_freq = 320
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> ACE
> begin time read from input coords = 2300.000 ps
>
>
> Number of triangulated 3-point waters found: 1846
>
> Sum of charges from parm topology file = 0.00000000
> Forcing neutrality...
>
> On Tue, Jun 11, 2024 at 12:06 AM Vinicius Cruzeiro <
> vcruzeiro.architecttherapeutics.com> wrote:
>
> Hello Dulal,
>
> Do you see any error messages at the bottom of your MDOUT files?
>
> Best,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Scientist II, Computational Chemistry
> Architect Therapeutics
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Dulal Mondal via AMBER <amber.ambermd.org>
> *Sent:* Monday, June 10, 2024 11:24 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] finddgref.py using pH-REMD
>
> Dear User,
>
> I am trying to find the reference energy of model Histidine. My group file
> is like below
> # Replica 001
> -O -i 001/001.in -p HIP_model.prmtop -c 001/nvtequi.ncrst -cpin HIP.cpin
> -o
> 001/mdout.rep.001 -cpout 001/cpout.rep.001 -cprestrt 001/cpin.rep.001 -r
> 001/ncrst.rep.001 -inf 001/mdinfo.rep.001 -x 001/nc.rep.001 -rem 4 -remlog
> rem.001.log
>
> # Replica 002
> -O -i 002/002.in -p HIP_model.prmtop -c 002/nvtequi.ncrst -cpin HIP.cpin
> -o
> 002/mdout.rep.001 -cpout 002/cpout.rep.001 -cprestrt 002/cpin.rep.001 -r
> 002/ncrst.rep.001 -inf 002/mdinfo.rep.001 -x 002/nc.rep.001 -rem 4 -remlog
> rem.001.log
>
> # Replica 003
> -O -i 003/003.in -p HIP_model.prmtop -c 003/nvtequi.ncrst -cpin HIP.cpin
> -o
> 003/mdout.rep.001 -cpout 003/cpout.rep.001 -cprestrt 003/cpin.rep.001 -r
> 003/ncrst.rep.001 -inf 003/mdinfo.rep.001 -x 003/nc.rep.001 -rem 4 -remlog
> rem.001.log
>
> # Replica 004
> -O -i 004/004.in -p HIP_model.prmtop -c 004/nvtequi.ncrst -cpin HIP.cpin
> -o
> 004/mdout.rep.001 -cpout 004/cpout.rep.001 -cprestrt 004/cpin.rep.001 -r
> 004/ncrst.rep.001 -inf 004/mdinfo.rep.001 -x 004/nc.rep.001 -rem 4 -remlog
> rem.001.log
>
> # Replica 005
> -O -i 005/005.in -p HIP_model.prmtop -c 005/nvtequi.ncrst -cpin HIP.cpin
> -o
> 005/mdout.rep.001 -cpout 005/cpout.rep.001 -cprestrt 005/cpin.rep.001 -r
> 005/ncrst.rep.001 -inf 005/mdinfo.rep.001 -x 005/nc.rep.001 -rem 4 -remlog
> rem.001.log
>
> # Replica 006
> -O -i 006/006.in -p HIP_model.prmtop -c 006/nvtequi.ncrst -cpin HIP.cpin
> -o
> 006/mdout.rep.001 -cpout 006/cpout.rep.001 -cprestrt 006/cpin.rep.001 -r
> 006/ncrst.rep.001 -inf 006/mdinfo.rep.001 -x 006/nc.rep.001 -rem 4 -remlog
> rem.001.log
>
> I got the following error
> Checking cpin file and/or cein file.
> We are going to find DELTAGREF for a pH titratable residue using Replica
> Exchange.
> The solvent pH value of replica 1 is 6.200 and was loaded from the
> mdin file (001/001.in).
> The solvent pH value of replica 2 is 6.400 and was loaded from the
> mdin file (002/002.in).
> The solvent pH value of replica 3 is 6.600 and was loaded from the
> mdin file (003/003.in).
> The solvent pH value of replica 4 is 6.800 and was loaded from the
> mdin file (004/004.in).
> The solvent pH value of replica 5 is 7.000 and was loaded from the
> mdin file (005/005.in).
> The solvent pH value of replica 6 is 7.200 and was loaded from the
> mdin file (006/006.in).
> The target pKa is 6.60000.
> The temperature is 300.00 K and was loaded from the mdin file (001/
> 001.in
> ).
> According to the mdin file (001/001.in), the value of ntcnstph is 500.
> According to the mdin file (001/001.in), the value of nstlim is 2000.
> According to the mdin file (001/001.in), the value of numexchg is 10000.
>
> The program will try to find a range of values for DELTAGREF
> automatically, as the argument -dgrefrange was not given
>
> AMBER execution #1: running 10000000 MD steps (5000 replica exchange
> attempts) for DELTAGREF = 0.000000 kcal/mol
>
> ERROR: The execution of AMBER using the binary
> /home/srabani/Downloads/amber18/bin/pmemd.cuda.MPI failed. The execution
> returned the following STDERR:
>
>
> --------------------------------------------------------------------------
>
>
> The command executed was:
>
> mpirun -np 6 /home/srabani/Downloads/amber18/bin/pmemd.cuda.MPI -ng
> 6 -groupfile groupfile001.temporary
>
> Check the mdout file (001/mdout.rep.001) to see what the error might
> be. Also check if all libraries necessary to run AMBER are properly set.
> The execution of finddgref.py stopped
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
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>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Jun 10 2024 - 22:30:03 PDT
