Re: [gmx-users] how to assign options of the same type?
If you use -deffnm it gives the same prefix to all files that are output (and requires the same prefix on the .tpr file that is input). For example, if your tpr file is md.ttr you could do gmx mdrun -deffnm md Your checkpoint files will be named md.cpt and your trr files will be named md.trr, as well as anything else that is being output as specified in the mdp file you used with grompp (energy files, gro files, xtc files, etc). -- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Sunday, May 24, 2015 7:55 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to assign options of the same type? On 5/24/15 8:29 AM, Zhang, Cheng wrote: Dear GROMACS, Can I ask how to assign options of the same type? For example, on the website of http://manual.gromacs.org/current/programs/gmx-mdrun.html It is said in the Synopsis: [-o [.trr/.cpt/...] I want to name the output files as md.trr and md.cpt. However, the followings do not work: -o md.trr md.cpt -o md.trr/md.cpt -o md.trr -o md.cpt So do you know what is the syntax? You can't specify multiple files to any option that is not labeled Mult. In the case of mdrun -o, that is the output trajectory format. The general help info in the synopsis indicates that this file type may be interchangeable in a general sense, but here it is somewhat misleading. You shouldn't try to output a checkpoint file in lieu of your trajectory. The .cpt is produced (automatically) with -cpo. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] how to assign options of the same type?
Dear GROMACS, Can I ask how to assign options of the same type? For example, on the website of http://manual.gromacs.org/current/programs/gmx-mdrun.html It is said in the Synopsis: [-o [.trr/.cpt/...] I want to name the output files as md.trr and md.cpt. However, the followings do not work: -o md.trr md.cpt -o md.trr/md.cpt -o md.trr -o md.cpt So do you know what is the syntax? Thank you very much. Yours sincerely Cheng -- 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] Can I ask how to extend my simulations?
Dear GROMACS, Can I ask how to extend my simulations? I would like to run a 50 ns job. Because of the cluster limitation, I need to use several jobs to complete that. ## Step1: grompp After using grompp on my PC, I got the input file md_0_1.tpr: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr ## Step2: mdrun As I see on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://manual.gromacs.org/current/programs/gmx-mdrun.html Can I ask if the following is correct in a job.sh file? (Initially, md_0_1.tpr and job.sh are the only files in the folder.) (I am still not sure how -cpi, -append, -maxh should be properly used. Do I also need to submit a second job with waiting dependency on the first job, what is the difference in the .sh file?) (In the following, if 24 hours is assigned to each job, can I still get the .xtc file after the first job has finished?) #!/bin/bash -l #$ -S /bin/bash #$ -l h_rt=24:00:0 #$ -l mem=4G #$ -l tmpfs=15G #$ -N MD #$ -pe openmpi 24 #$ -cwd module unload compilers module unload mpi module unload mkl module load compilers/intel/13.0/028_cxx11 module load mpi/openmpi/1.6.5/intel.13.0-028_cxx11 module load atlas/3.10.1/intel.13.0-028_cxx11 module load fftw/3.3.4/double/intel.13.0-028_cxx11 module load gromacs/5.0/openmpi/intel.13.0-028_cxx11 gerun mdrun_mpi -deffnm md_0_1 -cpi -maxh 23 ## Thank you very much. Yours sincerely Cheng -- 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] Can I ask how to extend my simulations?
On 5/24/15 11:57 AM, Zhang, Cheng wrote: Dear GROMACS, Can I ask how to extend my simulations? I would like to run a 50 ns job. Because of the cluster limitation, I need to use several jobs to complete that. ## Step1: grompp After using grompp on my PC, I got the input file md_0_1.tpr: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr ## Step2: mdrun As I see on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://manual.gromacs.org/current/programs/gmx-mdrun.html Can I ask if the following is correct in a job.sh file? (Initially, md_0_1.tpr and job.sh are the only files in the folder.) (I am still not sure how -cpi, -append, -maxh should be properly used. Do I also need to submit a second job with waiting dependency on the first job, what is the difference in the .sh file?) (In the following, if 24 hours is assigned to each job, can I still get the .xtc file after the first job has finished?) #!/bin/bash -l #$ -S /bin/bash #$ -l h_rt=24:00:0 #$ -l mem=4G #$ -l tmpfs=15G #$ -N MD #$ -pe openmpi 24 #$ -cwd module unload compilers module unload mpi module unload mkl module load compilers/intel/13.0/028_cxx11 module load mpi/openmpi/1.6.5/intel.13.0-028_cxx11 module load atlas/3.10.1/intel.13.0-028_cxx11 module load fftw/3.3.4/double/intel.13.0-028_cxx11 module load gromacs/5.0/openmpi/intel.13.0-028_cxx11 gerun mdrun_mpi -deffnm md_0_1 -cpi -maxh 23 -cpi -append are used for any subsequent extensions, not the first run. -cpi tells mdrun start from an existing checkpoint, not time zero. If there is no checkpoint, this is ignored. -maxh was designed to work in concert with wallclock limits. See the help text. -maxh 24 is safe here since your limit is 24 hours. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Doubt about correct system preparation sequence when protonation state calculation and ligand presence are involved
Hi everyone, I'm a little confused about the most correct sequence of the minimization, equilibration, solvatation and neutralization steps when I need to simulate a protein in a specific pH (through the protonation state calculation in this pH by using H++, for instance) and/or place a ligand in this protein (be it through covalent bonding or not). For instance, I've seen papers in which people use the following sequence: minimization, solvatation, H++ calculation, neutralization and equilibration, which is not so intuitive to me. Moreover, I've noticed that the sequence affects substantially the resulting protonation state in H++, but not so much the pI. So, I would like to know what is the most appropriate system preparation sequence for a protein simulation when I need it with the protonated state corresponding to a certain pH and when I need to place a certain ligand in this protein. I would be very grateful if someone could explain it me. Regards, Gustavo -- 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] End to end fixing
Dear Gromacs users, I have one protein which has the topological domain with two trans membrane domains. I would like to simulate the topological domain present in the cytosol. But here I can't do simulations as normals proteins. Because as the topological domain has trans membrane domains both sides, which suggests me that the ends should be fixed during simulations. The question is How do we fix the ends? means what should be the distance between the end? To solve this question I have looked into the NMR structure of the protein in PDB. The protein has 20 different conformational states. I checked the distance between the N'-terminal C-alpha and C'-terminal C-alpha. All the conformations showing large variance. How could I solve end-to-end fixing? Kindly tell me what can I do. Thanks in advane Surya Graduate student India. -- 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] Run NVT equilibrium
Thank a lot for your clearly explanation. Tuong Vy 2015-05-24 0:28 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/23/15 10:40 AM, Vy Phan wrote: Dear all, I wonder why , on some tutorial, running NVT equilibrium we need only the em.gro (the final coordinate of energy minimization step) . why do we not need em.edr ? Because there's no information in the .edr file that is needed to start NVT after EM. You only need the minimized coordinates at that point. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
