[gmx-users] Ionization: Your solvent group size (76663) is not a multiple of 3
Dear Gromacs users, I'm adding two different salts to my system in different concentrations; first salt addition is done successfully using the following commands: >gmx grompp -f em.mdp -c sys_solv.gro -p topol.top -o ions.tpr >gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG -pq 2 -nname CL -conc 0.1 -neutral For the second salt, I generated a new tpr file and used the following commands: >gmx grompp -f em.mdp -c sys_solv_ions.gro -p topol.top -o ions2.tpr gmx genion -s ions2.tpr -o sys_solv_ions.gro -p topol.top -pname NA -nname CL -conc 0.006 But for the second salt addition, I get a fatal error. Selected 4: 'SOL' --- Program: gmx genion, version 2016.3 Source file: src/gromacs/gmxana/gmx_genion.cpp (line 500) *Fatal error:Your solvent group size (76663) is not a multiple of 3* Any hints about this issue? Also, why should the solvent group size multiple of another number? Like, I have seen the case with other gromacs users: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-December/094291.html Thanks, Mohammed Sorour -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Ionization with different ions of different concentrations
Dear Gromacs users, I'm trying to add MgCl2 (100 mM) and NaCl (6 mM) to my system which has (-22 net charge). I add a neutralizing amount of Mg or Na using the genion neutral option. But when it comes to the salt concentration, I'm failing to have both of the salts added simultaneously. Like it will let me add Mgcl2 or Nacl. I use the following command: gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG -pq 2 -nname CL -conc 0.1 -neutral If I try to add Na and Mg at the same time: gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG -pq 2 -np 51 -nname CL -nn 82 -pname NA -np 2 I get the following message, which makes sense: Error in user input: Invalid command-line options In command-line option -pname Option specified multiple times In command-line option -np Option specified multiple times So my question is 1-Can we neutralize the system with different ions. like in my case (10 Na ions and 6 Mg ions)? 2-How can we add different salts with different concentrations? Thanks, Mohammed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Thank you so much, Carlos, using the full path helped me figure out the
problem.
So it turned out to be a problem with the path.
When using cd ${PBS_O_WORKDIR}/
it executes the job in my local directory --->
work/md/sequence_8_md/equilibration /nvt (When I made the directory
equilibration, I added a space at the end by mistake),
Renaming the equilibration directory and removing that space >
work/md/sequence_8_md/equilibration/nvt (That solved the problem and
the calculation is running)
Thank you so much, everyone!!
On Fri, Aug 2, 2019 at 11:34 AM Carlos Navarro
wrote:
> Did you try replacing the line
> cd ${PBS_O_WORKDIR}/
> with
> cd ‘YOUR_CURRENT_PATH’/
> ?
> Maybe as people already pointed out, the variable is not working properly.
> Maybe this could work.
> Best,
>
> ——
> Carlos Navarro Retamal
> Bioinformatic Engineering. PhD.
> Postdoctoral Researcher in Center of Bioinformatics and Molecular
> Simulations
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
> On August 2, 2019 at 5:20:33 PM, Mohammed I Sorour (
> mohammed.sor...@temple.edu) wrote:
>
> Yeah, I deeply appreciate your help. But any idea/recommendation why the
> same command doesn't work through the script? I can't run any jobs,
> especially such a big calculation, out of the queue system.
>
> On Fri, Aug 2, 2019 at 11:13 AM Justin Lemkul wrote:
>
> >
> >
> > On 8/2/19 11:09 AM, Mohammed I Sorour wrote:
> > > This is the output
> > >
> > >
> > > Begin Batch Job Epilogue Sat Aug 2 09:07:19 EDT 2019
> > > Job ID: 341185
> > > Username: tuf73544
> > > Group: chem
> > > Job Name: NVT
> > > Session: 45173
> > > Limits: walltime=01:00:00,neednodes=1:ppn=28,nodes=1:ppn=28
> > > Resources:
> > >
> >
> cput=19:59:39,vmem=1986008kb,walltime=00:42:53,mem=198008kb,energy_used=0
> > > Queue: normal
> > > Account:
> > > Deleting /dev/shm/*...
> > >
> > > End Batch Job Epilogue Sat Aug 2 09:08:39 EDT 2019
> > >
> > > Command line:
> > > gmx mdrun -deffnm nvt
> > >
> > >
> > > Running on 1 node with total 28 cores, 28 logical cores
> > > Hardware detected:
> > > CPU info:
> > > Vendor: Intel
> > > Brand: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz
> > > SIMD instructions most likely to fit this hardware: AVX2_256
> > > SIMD instructions selected at GROMACS compile time: SSE4.1
> > >
> > > Hardware topology: Full, with devices
> > >
> > > Compiled SIMD instructions: SSE4.1, GROMACS could use AVX2_256 on this
> > > machine, which is better.
> > >
> > > *Reading file nvt.tpr, VERSION 2016.3 (single precision)*
> > > Changing nstlist from 10 to 20, rlist from 1 to 1.029
> > >
> > > The number of OpenMP threads was set by environment variable
> > > OMP_NUM_THREADS to 1
> > >
> > > Will use 24 particle-particle and 4 PME only ranks
> > > This is a guess, check the performance at the end of the log file
> > > Using 28 MPI threads
> > > Using 1 OpenMP thread per tMPI thread
> > >
> > > starting mdrun 'DNA in water'
> > > 50 steps, 1000.0 ps.
> > >
> > > step 40 Turning on dynamic load balancing, because the performance
> loss
> > due
> > > to load imbalance is 4.1 %.
> > >
> > >
> > > Writing final coordinates.
> > >
> > > Average load imbalance: 1.5 %
> > > Part of the total run time spent waiting due to load imbalance: 1.2 %
> > > Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
> > X 0
> > > % Y 0 % Z 0 %
> > > Average PME mesh/force load: 0.752
> > > Part of the total run time spent waiting due to PP/PME imbalance: 3.1
> %
> > >
> > >
> > > Core t (s) Wall t (s) (%)
> > > Time: 71996.002 2571.286 2800.0
> > > 42:51
> > > (ns/day) (hour/ns)
> > > Performance: 33.602 0.714
> >
> > This output indicates that the job finished successfully and did not
> > produce the original error you posted.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Sounds great, thank you so much!! On Fri, Aug 2, 2019 at 11:21 AM Justin Lemkul wrote: > > > On 8/2/19 11:18 AM, Mohammed I Sorour wrote: > > Yeah, I deeply appreciate your help. But any idea/recommendation why the > > same command doesn't work through the script? I can't run any jobs, > > especially such a big calculation, out of the queue system. > > See my previous message about checking the working directory. Beyond > that, this is not a GROMACS problem - your system runs fine. Your > sysadmins are the people to ask about how to run jobs on your cluster. > > -Justin > > > On Fri, Aug 2, 2019 at 11:13 AM Justin Lemkul wrote: > > > >> > >> On 8/2/19 11:09 AM, Mohammed I Sorour wrote: > >>> This is the output > >>> > >>> > >>> Begin Batch Job Epilogue Sat Aug 2 09:07:19 EDT 2019 > >>> Job ID: 341185 > >>> Username: tuf73544 > >>> Group:chem > >>> Job Name: NVT > >>> Session: 45173 > >>> Limits: walltime=01:00:00,neednodes=1:ppn=28,nodes=1:ppn=28 > >>> Resources: > >>> > >> > cput=19:59:39,vmem=1986008kb,walltime=00:42:53,mem=198008kb,energy_used=0 > >>> Queue:normal > >>> Account: > >>> Deleting /dev/shm/*... > >>> > >>> End Batch Job Epilogue Sat Aug 2 09:08:39 EDT 2019 > >>> > >>> Command line: > >>> gmx mdrun -deffnm nvt > >>> > >>> > >>> Running on 1 node with total 28 cores, 28 logical cores > >>> Hardware detected: > >>> CPU info: > >>> Vendor: Intel > >>> Brand: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz > >>> SIMD instructions most likely to fit this hardware: AVX2_256 > >>> SIMD instructions selected at GROMACS compile time: SSE4.1 > >>> > >>> Hardware topology: Full, with devices > >>> > >>> Compiled SIMD instructions: SSE4.1, GROMACS could use AVX2_256 on this > >>> machine, which is better. > >>> > >>> *Reading file nvt.tpr, VERSION 2016.3 (single precision)* > >>> Changing nstlist from 10 to 20, rlist from 1 to 1.029 > >>> > >>> The number of OpenMP threads was set by environment variable > >>> OMP_NUM_THREADS to 1 > >>> > >>> Will use 24 particle-particle and 4 PME only ranks > >>> This is a guess, check the performance at the end of the log file > >>> Using 28 MPI threads > >>> Using 1 OpenMP thread per tMPI thread > >>> > >>> starting mdrun 'DNA in water' > >>> 50 steps, 1000.0 ps. > >>> > >>> step 40 Turning on dynamic load balancing, because the performance loss > >> due > >>> to load imbalance is 4.1 %. > >>> > >>> > >>> Writing final coordinates. > >>> > >>>Average load imbalance: 1.5 % > >>>Part of the total run time spent waiting due to load imbalance: 1.2 > % > >>>Steps where the load balancing was limited by -rdd, -rcon and/or > -dds: > >> X 0 > >>> % Y 0 % Z 0 % > >>>Average PME mesh/force load: 0.752 > >>>Part of the total run time spent waiting due to PP/PME imbalance: > 3.1 % > >>> > >>> > >>> Core t (s) Wall t (s)(%) > >>> Time:71996.002 2571.286 2800.0 > >>>42:51 > >>>(ns/day)(hour/ns) > >>> Performance: 33.6020.714 > >> This output indicates that the job finished successfully and did not > >> produce the original error you posted. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> Gromacs Users mailing list > >
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Yeah, I deeply appreciate your help. But any idea/recommendation why the same command doesn't work through the script? I can't run any jobs, especially such a big calculation, out of the queue system. On Fri, Aug 2, 2019 at 11:13 AM Justin Lemkul wrote: > > > On 8/2/19 11:09 AM, Mohammed I Sorour wrote: > > This is the output > > > > > > Begin Batch Job Epilogue Sat Aug 2 09:07:19 EDT 2019 > > Job ID: 341185 > > Username: tuf73544 > > Group:chem > > Job Name: NVT > > Session: 45173 > > Limits: walltime=01:00:00,neednodes=1:ppn=28,nodes=1:ppn=28 > > Resources: > > > cput=19:59:39,vmem=1986008kb,walltime=00:42:53,mem=198008kb,energy_used=0 > > Queue:normal > > Account: > > Deleting /dev/shm/*... > > > > End Batch Job Epilogue Sat Aug 2 09:08:39 EDT 2019 > > > > Command line: > >gmx mdrun -deffnm nvt > > > > > > Running on 1 node with total 28 cores, 28 logical cores > > Hardware detected: > >CPU info: > > Vendor: Intel > > Brand: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz > > SIMD instructions most likely to fit this hardware: AVX2_256 > > SIMD instructions selected at GROMACS compile time: SSE4.1 > > > >Hardware topology: Full, with devices > > > > Compiled SIMD instructions: SSE4.1, GROMACS could use AVX2_256 on this > > machine, which is better. > > > > *Reading file nvt.tpr, VERSION 2016.3 (single precision)* > > Changing nstlist from 10 to 20, rlist from 1 to 1.029 > > > > The number of OpenMP threads was set by environment variable > > OMP_NUM_THREADS to 1 > > > > Will use 24 particle-particle and 4 PME only ranks > > This is a guess, check the performance at the end of the log file > > Using 28 MPI threads > > Using 1 OpenMP thread per tMPI thread > > > > starting mdrun 'DNA in water' > > 50 steps, 1000.0 ps. > > > > step 40 Turning on dynamic load balancing, because the performance loss > due > > to load imbalance is 4.1 %. > > > > > > Writing final coordinates. > > > > Average load imbalance: 1.5 % > > Part of the total run time spent waiting due to load imbalance: 1.2 % > > Steps where the load balancing was limited by -rdd, -rcon and/or -dds: > X 0 > > % Y 0 % Z 0 % > > Average PME mesh/force load: 0.752 > > Part of the total run time spent waiting due to PP/PME imbalance: 3.1 % > > > > > > Core t (s) Wall t (s)(%) > > Time:71996.002 2571.286 2800.0 > > 42:51 > > (ns/day)(hour/ns) > > Performance: 33.6020.714 > > This output indicates that the job finished successfully and did not > produce the original error you posted. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
This is the output
Begin Batch Job Epilogue Sat Aug 2 09:07:19 EDT 2019
Job ID: 341185
Username: tuf73544
Group:chem
Job Name: NVT
Session: 45173
Limits: walltime=01:00:00,neednodes=1:ppn=28,nodes=1:ppn=28
Resources:
cput=19:59:39,vmem=1986008kb,walltime=00:42:53,mem=198008kb,energy_used=0
Queue:normal
Account:
Deleting /dev/shm/*...
End Batch Job Epilogue Sat Aug 2 09:08:39 EDT 2019
Command line:
gmx mdrun -deffnm nvt
Running on 1 node with total 28 cores, 28 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: SSE4.1
Hardware topology: Full, with devices
Compiled SIMD instructions: SSE4.1, GROMACS could use AVX2_256 on this
machine, which is better.
*Reading file nvt.tpr, VERSION 2016.3 (single precision)*
Changing nstlist from 10 to 20, rlist from 1 to 1.029
The number of OpenMP threads was set by environment variable
OMP_NUM_THREADS to 1
Will use 24 particle-particle and 4 PME only ranks
This is a guess, check the performance at the end of the log file
Using 28 MPI threads
Using 1 OpenMP thread per tMPI thread
starting mdrun 'DNA in water'
50 steps, 1000.0 ps.
step 40 Turning on dynamic load balancing, because the performance loss due
to load imbalance is 4.1 %.
Writing final coordinates.
Average load imbalance: 1.5 %
Part of the total run time spent waiting due to load imbalance: 1.2 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
% Y 0 % Z 0 %
Average PME mesh/force load: 0.752
Part of the total run time spent waiting due to PP/PME imbalance: 3.1 %
Core t (s) Wall t (s)(%)
Time:71996.002 2571.286 2800.0
42:51
(ns/day)(hour/ns)
Performance: 33.6020.714
On Fri, Aug 2, 2019 at 11:00 AM John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:
> > Hi Justin,
> >
> > Yes, I'm using a queuing system with a submission script.
> >
> > #-l nodes=1:ppn=16
> >
> > #PBS -l walltime=10:00:00
> >
> > #PBS -qmedium
> >
> > #PBS -N NVT
> >
> > #PBS -e out.err
> >
> > #PBS -o out
> >
> >
> >
> > module load gromacs
> >
> >
> > cd ${PBS_O_WORKDIR}/;
> >
> >
> > gmx mdrun -deffnm nvt
> >
> >
> > Well, based on your hint, I executed a trial mdrun job without using the
> > queue. It seems to be working well and reading the .tpr file, I had to
> > kill
> > the job once I made sure that it is reading the tpr file due to the
> > regulations of using the cluster out of the queue.
> > So, I should suspect that there is something wrong with executing the
> > script. It is worthy to note that I used the same script without any kind
> > of change multiple times and it's working well. This's more confusing for
> > me now, any hints?
>
> What is the output from the cluster? I'm guessing the output is in the
> file called "out" that's created each time the simulation fails.
>
>
> >
> > Thanks for the ionization/neutralization advice; surely I did that.
> >
> > Thanks,
> > Mohammed
> >
> > On Thu, Aug 1, 2019 at 9:22 PM Justin Lemkul wrote:
> >
> >>
> >>
> >> On 8/1/19 7:04 PM, Mohammed I Sorour wrote:
> >> >> Hi,
> >> >
> >> > that's what the ls -l prints,
> >> >
> >> >
> >> >
> >> >
> >> >> ls -l
> >> >> total 193120
> >> >> drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff
> >> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
> >> >> -rw-r--r-- 1 tuf73544 chem 191 Aug 1 15:04
> >> equilibration_NVT_script
> >> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro
> >> >> -rw-r--r-- 1 tuf73544 chem 2164 Jul 8 2016 ions.itp
> >> >> -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr
> >> >> -rw-r--r-- 1 tuf73544 chem11962 Aug 1 14:57 mdout.mdp
> >> >> -rw-r--r-- 1 tuf73544 chem11962 Aug 1 14:56 #mdout.mdp.1#
> >> >> -rw-r--r-- 1 tuf73544 chem 1875 Jul 27 08:22 nvt.mdp
> >> >> -rw-r--r-- 1 tuf73544 chem 39455312 Aug 1 14:57 nvt.tpr
> >> >> -rw--- 1 tuf73544 chem 1032 Aug 1 15:04 out
> >> >> -rw--- 1 tuf73544 chem 2395 Aug 1
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Hi Justin,
Yes, I'm using a queuing system with a submission script.
#-l nodes=1:ppn=16
#PBS -l walltime=10:00:00
#PBS -qmedium
#PBS -N NVT
#PBS -e out.err
#PBS -o out
module load gromacs
cd ${PBS_O_WORKDIR}/;
gmx mdrun -deffnm nvt
Well, based on your hint, I executed a trial mdrun job without using the
queue. It seems to be working well and reading the .tpr file, I had to kill
the job once I made sure that it is reading the tpr file due to the
regulations of using the cluster out of the queue.
So, I should suspect that there is something wrong with executing the
script. It is worthy to note that I used the same script without any kind
of change multiple times and it's working well. This's more confusing for
me now, any hints?
Thanks for the ionization/neutralization advice; surely I did that.
Thanks,
Mohammed
On Thu, Aug 1, 2019 at 9:22 PM Justin Lemkul wrote:
>
>
> On 8/1/19 7:04 PM, Mohammed I Sorour wrote:
> >> Hi,
> >
> > that's what the ls -l prints,
> >
> >
> >
> >
> >> ls -l
> >> total 193120
> >> drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff
> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
> >> -rw-r--r-- 1 tuf73544 chem 191 Aug 1 15:04
> equilibration_NVT_script
> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro
> >> -rw-r--r-- 1 tuf73544 chem 2164 Jul 8 2016 ions.itp
> >> -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr
> >> -rw-r--r-- 1 tuf73544 chem11962 Aug 1 14:57 mdout.mdp
> >> -rw-r--r-- 1 tuf73544 chem11962 Aug 1 14:56 #mdout.mdp.1#
> >> -rw-r--r-- 1 tuf73544 chem 1875 Jul 27 08:22 nvt.mdp
> >> -rw-r--r-- 1 tuf73544 chem 39455312 Aug 1 14:57 nvt.tpr
> >> -rw--- 1 tuf73544 chem 1032 Aug 1 15:04 out
> >> -rw--- 1 tuf73544 chem 2395 Aug 1 15:04 out.err
> >> -rw-r--r-- 1 tuf73544 chem38899 Jul 31 18:58 posre_DNA_chain_A.itp
> >> -rw-r--r-- 1 tuf73544 chem39953 Jul 31 18:58 posre_DNA_chain_B.itp
> >> -rw-r--r-- 1 tuf73544 chem 3215 Aug 1 14:57 residuetypes.dat
> >> -rw-r--r-- 1 tuf73544 chem 4873 Jul 18 13:03 specbond.dat
> >> -rw-r--r-- 1 tuf73544 chem69176 Jul 16 11:40 tip3p.gro
> >> -rw-r--r-- 1 tuf73544 chem 588482 Jul 31 18:58 topol_DNA_chain_A.itp
> >> -rw-r--r-- 1 tuf73544 chem 589283 Jul 31 18:58 topol_DNA_chain_B.itp
> >> -rw--- 1 tuf73544 chem 1264 Jul 31 19:10 topol.top
> >> drwxr-xr-x 3 tuf73544 chem 4096 Aug 1 14:18 trial
>
> Are you executing mdrun interactively, or via some kind of queuing
> system with a submission script?
>
> Also you should *not* be running dynamics on a system with such a net
> charge. Add salt and neutralize! It's not the source of your problem,
> though.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
> > Hi, that's what the ls -l prints, > > ls -l > total 193120 > drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff > -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro > -rw-r--r-- 1 tuf73544 chem 191 Aug 1 15:04 equilibration_NVT_script > -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro > -rw-r--r-- 1 tuf73544 chem 2164 Jul 8 2016 ions.itp > -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr > -rw-r--r-- 1 tuf73544 chem11962 Aug 1 14:57 mdout.mdp > -rw-r--r-- 1 tuf73544 chem11962 Aug 1 14:56 #mdout.mdp.1# > -rw-r--r-- 1 tuf73544 chem 1875 Jul 27 08:22 nvt.mdp > -rw-r--r-- 1 tuf73544 chem 39455312 Aug 1 14:57 nvt.tpr > -rw--- 1 tuf73544 chem 1032 Aug 1 15:04 out > -rw--- 1 tuf73544 chem 2395 Aug 1 15:04 out.err > -rw-r--r-- 1 tuf73544 chem38899 Jul 31 18:58 posre_DNA_chain_A.itp > -rw-r--r-- 1 tuf73544 chem39953 Jul 31 18:58 posre_DNA_chain_B.itp > -rw-r--r-- 1 tuf73544 chem 3215 Aug 1 14:57 residuetypes.dat > -rw-r--r-- 1 tuf73544 chem 4873 Jul 18 13:03 specbond.dat > -rw-r--r-- 1 tuf73544 chem69176 Jul 16 11:40 tip3p.gro > -rw-r--r-- 1 tuf73544 chem 588482 Jul 31 18:58 topol_DNA_chain_A.itp > -rw-r--r-- 1 tuf73544 chem 589283 Jul 31 18:58 topol_DNA_chain_B.itp > -rw--- 1 tuf73544 chem 1264 Jul 31 19:10 topol.top > drwxr-xr-x 3 tuf73544 chem 4096 Aug 1 14:18 trial > Thanks, Mohammed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Hello Dr. Dallas, Yes, the nvt.tpr was created and I had it in the local directory ready for the mdrun. Yes, those copy/pastes of the commands I used. Since I'm kind of new to the MD simulations, so I'm sticking to that tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html . Also, I tried to use the mdrun command in a different way just to give it a try command: gmx mdrun -s nvt.tpr -deffnm nvt It gave me the following error. Error in user input: Invalid command-line options In command-line option -s File 'nvt.tpr' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2) I know that it is clearly saying that nvt.tpr is not there. But I'm also sure that I have it there. Thanks, Mohammed On Thu, Aug 1, 2019 at 6:40 PM Dallas Warren wrote: > From that command, was the nvt.tpr actually created? Can you see it in the > directory? What happens if you type in the files for each of the command > switches instead of using -deffnm to autocomplete them for you? > > Are those copy/pastes of the commands you used? > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On Fri, 2 Aug 2019 at 08:30, Mohammed I Sorour > > wrote: > > > Hi Justin, > > > > Thank you so much for your reply. > > > > for the NVT run, I used the following commands > > > > *gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr* > > > > which generated the nvt.tpr file and printed the following: > > > > Ignoring obsolete mdp entry 'title' > > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# > > Setting the LD random seed to 708625668 > > Generated 4851 of the 4851 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 4851 of the 4851 1-4 parameter combinations > > Excluding 3 bonded neighbours molecule type 'DNA_chain_B' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'DNA_chain_A' > > turning all bonds into constraints... > > Excluding 2 bonded neighbours molecule type 'SOL' > > turning all bonds into constraints... > > Excluding 1 bonded neighbours molecule type 'MG' > > turning all bonds into constraints... > > Excluding 1 bonded neighbours molecule type 'CL' > > turning all bonds into constraints... > > > > NOTE 1 [file topol.top, line 51]: > > System has non-zero total charge: -117.68 > > Total charge should normally be an integer. See > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > for discussion on how close it should be to an integer. > > > > > > > > Setting gen_seed to -1290262031 > > Velocities were taken from a Maxwell distribution at 300 K > > Removing all charge groups because cutoff-scheme=Verlet > > Analysing residue names: > > There are: 124DNA residues > > There are: 455308 Water residues > > Number of degrees of freedom in T-Coupling group DNA is 7631.99 > > Number of degrees of freedom in T-Coupling group Water is 2724393.00 > > Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K > > Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036 nm > > Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm > > Note that mdrun will redetermine rlist based on the actual pair-list > setup > > Calculating fourier grid dimensions for X Y Z > > Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150 > > Estimate for the relative computational load of the PME mesh part: 0.16 > > > > NOTE 2 [file nvt.mdp]: > > This run will generate roughly 31380 Mb of data > > > > > > There were 2 notes > > > > GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa) > > > > *Then I used the mdrun command * > > > > *gmx mdrun -deffnm nvt* > > > > > > > > Again, I have run a couple of systems before that and I successfully ran > > the MD_production calculation, following the same procedure. The only > > difference I could notice is the charges rounding, because it didn't > happen > > with those that ran successfully. That is why I suspected that. > > > > Please, let me know if
Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Hi Justin, Thank you so much for your reply. for the NVT run, I used the following commands *gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr* which generated the nvt.tpr file and printed the following: Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# Setting the LD random seed to 708625668 Generated 4851 of the 4851 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4851 of the 4851 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA_chain_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'DNA_chain_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'MG' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... NOTE 1 [file topol.top, line 51]: System has non-zero total charge: -117.68 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Setting gen_seed to -1290262031 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 124DNA residues There are: 455308 Water residues Number of degrees of freedom in T-Coupling group DNA is 7631.99 Number of degrees of freedom in T-Coupling group Water is 2724393.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150 Estimate for the relative computational load of the PME mesh part: 0.16 NOTE 2 [file nvt.mdp]: This run will generate roughly 31380 Mb of data There were 2 notes GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa) *Then I used the mdrun command * *gmx mdrun -deffnm nvt* Again, I have run a couple of systems before that and I successfully ran the MD_production calculation, following the same procedure. The only difference I could notice is the charges rounding, because it didn't happen with those that ran successfully. That is why I suspected that. Please, let me know if I need to provide more information. Thanks, Mohammed On Thu, Aug 1, 2019 at 3:52 PM Justin Lemkul wrote: > > > On 8/1/19 3:50 PM, Mohammed I Sorour wrote: > > Dear Gromacs users, > > > > I'm running MD simulation on a couple of DNA systems that only vary in > > sequence. Most of the runs worked just fine, but surprisingly I have one > > system that I got an error in the NVT equilibration step. > > I'm following the > > tutorialhttp:// > www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html > > > > rogram: gmx mdrun, version 2016.3 > > Source file: src/gromacs/options/options.cpp (line 258) > > Function:void gmx::Options::finish() > > > > Error in user input: > > Invalid input values > >In option s > > Required option was not provided, and the default file 'topol' does > not > > exist or is not accessible. > > The following extensions were tried to complete the file name: > >.tpr > > > > I'm pretty sure that I have the .tpr files in the local directory. I > have > > read the previous reviews of the Gromacs mailing list, and I know that > > it would be a problem with the toplogy file. The toplogy files looks > > so far good to me. > > There's a typo in your command or the input file you think is there is > not. You didn't provide your mdrun command (please always do this) but I > suspect the former. If mdrun does not find the file you specify, it > looks for the default file name, which is topol.tpr. That's also not > there, so you get a fatal error. > > > Here is the only thing I can susbect, but I don't know if this is the > > cause, but also I'm still wondering why: So When I generated my ssytem > > topology using pdb2gmx > > > > > > "Now there are 3969 atoms and 124 residues > > Total mass in system 37825.764 a.m.u. > > Total charge in system -118.000 e" > > > > But when I start the solvation, the total charge of the system changes > > and is no more an intger: > > > > "NOTE 2 [file topol.top, line 51]: > >System has non-zero total charge: -117.68 > >Total charge should normally b
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges
Dear Gromacs users, I'm running MD simulation on a couple of DNA systems that only vary in sequence. Most of the runs worked just fine, but surprisingly I have one system that I got an error in the NVT equilibration step. I'm following the tutorialhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html rogram: gmx mdrun, version 2016.3 Source file: src/gromacs/options/options.cpp (line 258) Function:void gmx::Options::finish() Error in user input: Invalid input values In option s Required option was not provided, and the default file 'topol' does not exist or is not accessible. The following extensions were tried to complete the file name: .tpr I'm pretty sure that I have the .tpr files in the local directory. I have read the previous reviews of the Gromacs mailing list, and I know that it would be a problem with the toplogy file. The toplogy files looks so far good to me. Here is the only thing I can susbect, but I don't know if this is the cause, but also I'm still wondering why: So When I generated my ssytem topology using pdb2gmx "Now there are 3969 atoms and 124 residues Total mass in system 37825.764 a.m.u. Total charge in system -118.000 e" But when I start the solvation, the total charge of the system changes and is no more an intger: "NOTE 2 [file topol.top, line 51]: System has non-zero total charge: -117.68 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer." >From the gromacs documentations, it's fine to have that slight non-integer charge, but I'm wondering why is that happening?! I ran the energy minimization using these files, and it worked well, it only failing with the NVT step. I deeply aplogize for the lenghty email and for submitting the same email previously. The first one was not complete and was sent by mistake. Sincerely, Mohammed Sorour -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible
Dear Gromacs users, I'm running MD simulation on a couple of DNA systems that only vary in sequence. Most of the runs worked just fine, but surprisingly I have one system that I got an error in the NVT equilibration step. I'm following the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html rogram: gmx mdrun, version 2016.3 Source file: src/gromacs/options/options.cpp (line 258) Function:void gmx::Options::finish() Error in user input: Invalid input values In option s Required option was not provided, and the default file 'topol' does not exist or is not accessible. The following extensions were tried to complete the file name: .tpr I'm pretty sure that I have the .tpr files in the local directory. I have read the previous reviews of the Gromacs mailing list, but I -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
