Re: [gmx-users] pdb2gmx input file error
Hi Acoot, What do you mean with 'not at all'? What is the output of pdb2gmx? Did you check what is in those pdb files? Cheers, Tsjerk On Mar 22, 2012 5:06 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, I find some pdb files downloaded from RCSB cannot be recognized by pdb2gmx at all. Is any server which can convert and RCSB pdb files to files readable by pdb2gmx? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] continue replica exchange MD
On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas a.ku...@herts.ac.uk wrote:
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1
-cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e
edrRemd_20ns.edr -stepout 2000
From my side, I have no problem resuming or extending the REMD
simulations in V.4.5.5 and 4.5.4
Here is the command:
mdrun_g_f -s md_.tpr -multi 32 -replex 500 -cpi state_.cpt -append
I use state_.cpt, not state.cpt
I get the following output:
**
...
...
500 steps, 1.0 ps (continuing from step 49430, 98.9 ps).
500 steps, 1.0 ps (continuing from step 49430, 98.9 ps).
step 49430, will finish Wed Sep 12 16:09:33 2012
step 5, will finish Thu May 24 11:23:04 2012
Step 47546: resetting all time and cycle counters
= PBS: job killed: walltime 604823 exceeded limit 604800
Terminated
**
Apparently, the job runs for one week on a computer cluster (that is the
maximum time allowed), but it does not progress very much beyond step 49430.
Also the log-file does not show any more steps:
Step Time Lambda
46455 92.91000 0.0
Grid: 18 x 17 x 25 cells
Energies (kJ/mol)
G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.83095e+04 3.70277e+04 2.14102e+03 8.83853e+03 -7.33070e+02
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
2.29503e+05 3.04138e+05 -2.66781e+04 -8.51221e+03 -2.74692e+06
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-9.59421e+05 5.41532e+03 -3.09689e+06 5.18959e+05 -2.57793e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97550e+02 -1.14933e+02 5.41944e+01 0.0e+00
Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012
---
Restarting from checkpoint, appending to previous log file.
...
...
Started mdrun on node 0 Tue Mar 6 16:40:10 2012
Step Time Lambda
49430 98.86000 0.0
Grid: 18 x 17 x 25 cells
Energies (kJ/mol)
G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.84241e+04 3.69121e+04 2.09533e+03 8.80916e+03 -4.67086e+02
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
2.29528e+05 2.99825e+05 -2.67028e+04 -8.51334e+03 -2.74410e+06
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-9.59506e+05 5.47116e+03 -3.09823e+06 5.18993e+05 -2.57923e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97570e+02 -1.14963e+02 2.67842e+00 0.0e+00
Step Time Lambda
5 100.0 0.0
Energies (kJ/mol)
G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.86161e+04 3.71585e+04 2.15336e+03 8.92946e+03 -4.84684e+02
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
2.29950e+05 3.01014e+05 -2.66724e+04 -8.51306e+03 -2.74349e+06
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-9.59537e+05 5.56712e+03 -3.09531e+06 5.19371e+05 -2.57594e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97787e+02 -1.14956e+02 2.36460e+01 1.50068e-05
[End of log-file]
***
I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem
or maybe a problem of the computer cluster (MPI, etc). I would be grateful
for any help.
Many thanks
Andreas--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] a question related to energy minimization mdrun -v -deffnm em
Dear All, I am running energy minimization mdrun -v -deffnm em. The number of atoms in my system is far more than 4018, especially after the water box edded. However in the mdrun -v -deffnm em running process, the screen shows Step= 816, Dmax= 1.9e-02 nm, Epot= -3.04546e+06 Fmax= 1.54937e+04, atom= 4018. Will you please tell me why the atom number is only 4018? Have I done something wrong? Cheers, Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
This days I tested some distance restrains applied on my protein. I had some literature data from wich I've used such restrains as well as similar wirk where authors applied this data on the same protein to view some biological-relevant event :) I've applied my restrains gradually to rise force from 0.1 to 30 kj nm mol in mdp file. During such task I've noticed some disagreements between distances wich I obtained after simulation as well as experimetnal data E.g in the topology file I've defined 2 restrains 1258 2203 115 1 0.450 0.650 1.600 1.0 1255 2742 116 1 1.900 2.150 3.150 1.0 In this case this means that I defined first restrains betwenn 0.45r1 0.65 where the value 1.600 is another threshold after wich forses rise more gradually ( linnear). So I thought that the forces must restrain the distance in the range between r0 and r1 most strongly. The second restrain was chosen in the similar manner. But when I've checked output gro file I've found that real distances between first two atoms were 0.800 nm ( 0.650) and betwen the second pair of atoms 1.5 ( less than lowest R0 threshold 1.9 ). Why such disagreements have been occured ? Should I define restrains range more accurately ? (e.g if I want to restrain atoms in the distance equal to 0.5 nm so such harmonic restrains should be 0.45 0.55 for r0 and r1 respectyally. ) Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question related to energy minimization mdrun -v -deffnm em
The output of energy minimization displays the atom with the highest forces on it for that particular step. It does not reflect the size of the system. On 2012-03-22 12:09:15AM -0700, Acoot Brett wrote: Dear All, I am running energy minimization mdrun -v -deffnm em. The number of atoms in my system is far more than 4018, especially after the water box edded. However in the mdrun -v -deffnm em running process, the screen shows Step= 816, Dmax= 1.9e-02 nm, Epot= -3.04546e+06 Fmax= 1.54937e+04, atom= 4018. Will you please tell me why the atom number is only 4018? Have I done something wrong? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx input file error
Dear All, The problem has been solved. When I cp the pdb file from another folder to the gromacs running folder, I find the pdb file in the gromacs running folder was not permitted to open, even by vi.. Then in the normal Windows system I copy the pdb file in its original folder and paste it into the gromacs running folder, in cygwin gromcas the pab can be read (or can be open by vi). But there is still ununderstandable why by cp the pdb file is not permitted to open. Cheers, Acoot From: Tsjerk Wassenaar tsje...@gmail.com To: Acoot Brett acootbr...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 22 March 2012 4:24 PM Subject: Re: [gmx-users] pdb2gmx input file error Hi Acoot, What do you mean with 'not at all'? What is the output of pdb2gmx? Did you check what is in those pdb files? Cheers, Tsjerk On Mar 22, 2012 5:06 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, I find some pdb files downloaded from RCSB cannot be recognized by pdb2gmx at all. Is any server which can convert and RCSB pdb files to files readable by pdb2gmx? Cheers, Acoot -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Erroneous bond in average pdb
Hi Gromacs Specialist, I want to study protein aggregation study. 1. after giving the command g_anaeig -v .. -s .. -f .. -first 1 -last 1 -nframe 100 -extr ev1.pdb I got the pdb structure having 100 frame , but the structure have erroneous bonds, I try both VMD and pymol, but but get the same , What to do to solve problem ?? Should I have to do energy minimisation(IS it good idea???) ??? 2. My RMSD is fluctuating in the range of 0.7 nm As it is generally consider good to have RMSD less than 0.4 nm in MD Is it the ok to study protein aggregation study or any wrong happened?? Thank you in Advance.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx input file error
On 22/03/2012 6:15 PM, Acoot Brett wrote: Dear All, The problem has been solved. When I cp the pdb file from another folder to the gromacs running folder, I find the pdb file in the gromacs running folder was not permitted to open, even by vi.. Then in the normal Windows system I copy the pdb file in its original folder and paste it into the gromacs running folder, in cygwin gromcas the pab can be read (or can be open by vi). But there is still ununderstandable why by cp the pdb file is not permitted to open. Sounds like you have done something inappropriate with file and/or directory permissions, perhaps by changing which Windows user did what at which time. It's not a GROMACS problem, anyway. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Erroneous bond in average pdb
On 22/03/2012 9:10 PM, rama david wrote: Hi Gromacs Specialist, I want to study protein aggregation study. 1. after giving the command g_anaeig -v .. -s .. -f .. -first 1 -last 1 -nframe 100 -extr ev1.pdb I got the pdb structure having 100 frame , but the structure have erroneous bonds, I try both VMD and pymol, but but get the same , What to do to solve problem ?? See http://www.gromacs.org/Documentation/FAQs Analysis and visualization number 8 to understand whether you have a problem. Mark Should I have to do energy minimisation(IS it good idea???) ??? 2. My RMSD is fluctuating in the range of 0.7 nm As it is generally consider good to have RMSD less than 0.4 nm in MD Is it the ok to study protein aggregation study or any wrong happened?? Thank you in Advance.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
On 22/03/2012 6:12 PM, James Starlight wrote: This days I tested some distance restrains applied on my protein. I had some literature data from wich I've used such restrains as well as similar wirk where authors applied this data on the same protein to view some biological-relevant event :) I've applied my restrains gradually to rise force from 0.1 to 30 kj nm mol in mdp file. During such task I've noticed some disagreements between distances wich I obtained after simulation as well as experimetnal data E.g in the topology file I've defined 2 restrains 1258 2203 115 1 0.450 0.650 1.600 1.0 1255 2742 116 1 1.900 2.150 3.150 1.0 In this case this means that I defined first restrains betwenn 0.45r1 0.65 where the value 1.600 is another threshold after wich forses rise more gradually ( linnear). So I thought that the forces must restrain the distance in the range between r0 and r1 most strongly. The second restrain was chosen in the similar manner. The position restraint forces are zero between r0 and r1, not restraining... most strongly there. But when I've checked output gro file I've found that real distances between first two atoms were 0.800 nm ( 0.650) and betwen the second pair of atoms 1.5 ( less than lowest R0 threshold 1.9 ). Why such disagreements have been occured ? Should I define restrains range more accurately ? (e.g if I want to restrain atoms in the distance equal to 0.5 nm so such harmonic restrains should be 0.45 0.55 for r0 and r1 respectyally. ) If there's a car at the bottom of one valley in the Alps, and you think it should be two valleys over, and you pull it with a trained cat... it's not going to move much. How big an animal you need depends on the geography. There need not even be a reasonable route for you to take, if the target valley is effectively on Mars. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Editing the functions of amber
Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhi asaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Editing the functions of amber
On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Editing the functions of amber
Dear Matt Thank you very much for the reply. About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy. Can this be done with the table lookups? Are you willing to cooperate with us on 2? Thanks Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 4:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Editing the functions of amber
On 23/03/2012 1:59 AM, Asaf Farhi wrote: Dear Matt Thank you very much for the reply. About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy. Can this be done with the table lookups? Yes, any potential that is a function of distance between pairs can be done. See manual 6.7.2. Of course, plain cut-offs can be done without tables since about 1976... Are you willing to cooperate with us on 2? I don't have time for new projects, but a post to gmx-developers may elicit feedback on feasibility. Mark Thanks Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 4:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear Gromacs users,
I am performing MD simulation of an 14 units oligosaccharide on Gromacs
4.5.4. I am able to successfully do a 10 ns simulation on a DELL-precision
workstation and also a 5ns simulation on tyrone cluster using a PBS script
(shown below). However, when I am trying to proceed for further consecutive
5ns simulation, I get an error saying no domain decompositions error. I
have tried changing the number of nodes by making it to 16 but it showed
the same error. whereas, when I tried it on the same workstation as before,
the mdrun has successfully executed. Please help me in letting me know what
is the problem with the system and what parameters or argument I am missing
while running it in tyrone cluster. I am providing the md.mdp parameter and
the PBS script are also provided as attachments to this mail
*
**the error is:*
Program mdrun_mpi_d, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 32 nodes that is compatible with the
given box and a minimum cell size of 1.33444 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
*and the PBS script is as below:*
#!/bin/sh
#PBS -N test
#PBS -l nodes=1:ppn=32:debug
#PBS -l walltime=2:00:00
#PBS -S /bin/sh
#PBS -j oe
curr_dir=${PBS_O_WORKDIR}
cd ${PBS_O_WORKDIR}
NPROCS='wc -l $PBC_NODEFILE'
HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' '
echo Running Directory is 'pwd'
/opt/mvapich2-1.7rc1/gcc/bin/mpirun -np 32
/home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d -deffnm
triglc-MD4 -c triglc-MD6.pdb
*Please suggest me how to resolve this error.
*
Thank you in advance.
Dr. M. Asha Latha Sreshty,
PDF,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore,
INDIA
test.o4101
Description: Binary data
md.mdp
Description: Binary data
test3.sh
Description: Bourne shell script
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] continue replica exchange MD
22 mar 2012 kl. 08.05 skrev lina:
On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas a.ku...@herts.ac.uk wrote:
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1
-cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e
edrRemd_20ns.edr -stepout 2000
From my side, I have no problem resuming or extending the REMD
simulations in V.4.5.5 and 4.5.4
I've had problems with continuation of REMD simulations with gmx 4.5.5
(although manifested differently IIRC). The release-4-5-patches contain
bugfixes that solved the problems. I suggest trying the patches.
Erik
Here is the command:
mdrun_g_f -s md_.tpr -multi 32 -replex 500 -cpi state_.cpt -append
I use state_.cpt, not state.cpt
I get the following output:
**
...
...
500 steps, 1.0 ps (continuing from step 49430, 98.9 ps).
500 steps, 1.0 ps (continuing from step 49430, 98.9 ps).
step 49430, will finish Wed Sep 12 16:09:33 2012
step 5, will finish Thu May 24 11:23:04 2012
Step 47546: resetting all time and cycle counters
= PBS: job killed: walltime 604823 exceeded limit 604800
Terminated
**
Apparently, the job runs for one week on a computer cluster (that is the
maximum time allowed), but it does not progress very much beyond step 49430.
Also the log-file does not show any more steps:
Step Time Lambda
46455 92.910000.0
Grid: 18 x 17 x 25 cells
Energies (kJ/mol)
G96AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.83095e+043.70277e+042.14102e+038.83853e+03 -7.33070e+02
Coulomb-14LJ (SR)LJ (LR) Disper. corr. Coulomb (SR)
2.29503e+053.04138e+05 -2.66781e+04 -8.51221e+03 -2.74692e+06
Coul. recip. Position Rest. PotentialKinetic En. Total Energy
-9.59421e+055.41532e+03 -3.09689e+065.18959e+05 -2.57793e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97550e+02 -1.14933e+025.41944e+010.0e+00
Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012
---
Restarting from checkpoint, appending to previous log file.
...
...
Started mdrun on node 0 Tue Mar 6 16:40:10 2012
Step Time Lambda
49430 98.860000.0
Grid: 18 x 17 x 25 cells
Energies (kJ/mol)
G96AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.84241e+043.69121e+042.09533e+038.80916e+03 -4.67086e+02
Coulomb-14LJ (SR)LJ (LR) Disper. corr. Coulomb (SR)
2.29528e+052.99825e+05 -2.67028e+04 -8.51334e+03 -2.74410e+06
Coul. recip. Position Rest. PotentialKinetic En. Total Energy
-9.59506e+055.47116e+03 -3.09823e+065.18993e+05 -2.57923e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97570e+02 -1.14963e+022.67842e+000.0e+00
Step Time Lambda
5 100.00.0
Energies (kJ/mol)
G96AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.86161e+043.71585e+042.15336e+038.92946e+03 -4.84684e+02
Coulomb-14LJ (SR)LJ (LR) Disper. corr. Coulomb (SR)
2.29950e+053.01014e+05 -2.66724e+04 -8.51306e+03 -2.74349e+06
Coul. recip. Position Rest. PotentialKinetic En. Total Energy
-9.59537e+055.56712e+03 -3.09531e+065.19371e+05 -2.57594e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97787e+02 -1.14956e+022.36460e+011.50068e-05
[End of log-file]
***
I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem
or maybe a problem of the computer cluster (MPI, etc). I would be grateful
for any help.
Many thanks
Andreas--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read
Re: [gmx-users] Error: no domain decomposition, Source code file: domdec.c, line: 6436
On 23/03/2012 2:14 AM, Ashalatha Sreshty wrote:
Dear Gromacs users,
I am performing MD simulation of an 14 units oligosaccharide on
Gromacs 4.5.4. I am able to successfully do a 10 ns simulation on a
DELL-precision workstation and also a 5ns simulation on tyrone cluster
using a PBS script (shown below). However, when I am trying to proceed
for further consecutive 5ns simulation, I get an error saying no
domain decompositions error. I have tried changing the number of nodes
by making it to 16 but it showed the same error. whereas, when I tried
it on the same workstation as before, the mdrun has successfully
executed. Please help me in letting me know what is the problem with
the system and what parameters or argument I am missing while running
it in tyrone cluster. I am providing the md.mdp parameter and the PBS
script are also provided as attachments to this mail
*
**the error is:*
Program mdrun_mpi_d, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 32 nodes that is compatible with
the given box and a minimum cell size of 1.33444 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
Following this link will lead you to a further link with some helpful
discussion.
Mark
*and the PBS script is as below:*
#!/bin/sh
#PBS -N test
#PBS -l nodes=1:ppn=32:debug
#PBS -l walltime=2:00:00
#PBS -S /bin/sh
#PBS -j oe
curr_dir=${PBS_O_WORKDIR}
cd ${PBS_O_WORKDIR}
NPROCS='wc -l $PBC_NODEFILE'
HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' '
echo Running Directory is 'pwd'
/opt/mvapich2-1.7rc1/gcc/bin/mpirun -np 32
/home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d -deffnm
triglc-MD4 -c triglc-MD6.pdb
*Please suggest me how to resolve this error.
*
Thank you in advance.
Dr. M. Asha Latha Sreshty,
PDF,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore,
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Editing the functions of amber
Thank you very much for the reply. I tried to send this question few days ago and they said that I'm not allowed to post there. (The edition of the replica exchange shouldn't be complicated.) Do you have any tips regarding what I should do? Thanks in advance, Best regards, Asaf_ ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 5:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 1:59 AM, Asaf Farhi wrote: Dear Matt Thank you very much for the reply. About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy. Can this be done with the table lookups? Yes, any potential that is a function of distance between pairs can be done. See manual 6.7.2. Of course, plain cut-offs can be done without tables since about 1976... Are you willing to cooperate with us on 2? I don't have time for new projects, but a post to gmx-developers may elicit feedback on feasibility. Mark Thanks Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 4:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] Editing the functions of amber
On 23/03/2012 2:56 AM, Asaf Farhi wrote: Thank you very much for the reply. I tried to send this question few days ago and they said that I'm not allowed to post there. (The edition of the replica exchange shouldn't be complicated.) Do you have any tips regarding what I should do? Read the RE documentation the manual and mdrun -h. Get out a debugger and step through the code. Most of the stuff relevant to replica exchange is in src/kernel/repl_ex.c Mark Thanks in advance, Best regards, Asaf_ ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 5:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 1:59 AM, Asaf Farhi wrote: Dear Matt Thank you very much for the reply. About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy. Can this be done with the table lookups? Yes, any potential that is a function of distance between pairs can be done. See manual 6.7.2. Of course, plain cut-offs can be done without tables since about 1976... Are you willing to cooperate with us on 2? I don't have time for new projects, but a post to gmx-developers may elicit feedback on feasibility. Mark Thanks Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 4:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
RE: [gmx-users] Editing the functions of amber
Thank you very much. Have a nice weekend, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 5:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 2:56 AM, Asaf Farhi wrote: Thank you very much for the reply. I tried to send this question few days ago and they said that I'm not allowed to post there. (The edition of the replica exchange shouldn't be complicated.) Do you have any tips regarding what I should do? Read the RE documentation the manual and mdrun -h. Get out a debugger and step through the code. Most of the stuff relevant to replica exchange is in src/kernel/repl_ex.c Mark Thanks in advance, Best regards, Asaf_ ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 5:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 1:59 AM, Asaf Farhi wrote: Dear Matt Thank you very much for the reply. About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy. Can this be done with the table lookups? Yes, any potential that is a function of distance between pairs can be done. See manual 6.7.2. Of course, plain cut-offs can be done without tables since about 1976... Are you willing to cooperate with us on 2? I don't have time for new projects, but a post to gmx-developers may elicit feedback on feasibility. Mark Thanks Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 4:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how to do it? Thanks in advance, Best regards, Asaf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Box Size in MD
Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box Size in MD
As far as I concern, the minimum size is that cove all parts of your molecules or system. In case you should use solvent it is up to you to add how many molecules and in this case you should make decision by experience or according to literature. Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 22, 2012 at 12:08 PM, Lara Bunte lara.bu...@yahoo.de wrote: Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box Size in MD
Hi Lara, The cut-offs are pretty much part of the force field. One rule is that the distance between periodic images should be larger than the cutoff. For protein/solute simulations that translates in a minimal distance between the solute and the wall of half the cutoff used. Another rule is based on the solvent ordering. In water, ordering carries through approximately four layers of water, corresponding to 1 nm. So to avoid indirect effects through solvent ordering, it is advisable to use a distance between periodic images of 2 nm, i.e. a distance between solute and box wall of 1 nm. Hope it helps, Tsjerk On Thu, Mar 22, 2012 at 5:08 PM, Lara Bunte lara.bu...@yahoo.de wrote: Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? Thanks for help Greetings Lara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box Size in MD
Lara Bunte wrote: Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? This is not correct. The cutoffs are dictated by the force field you've chosen to use. There are predefined values that should (for the most part) be adhered to. What you need to make sure of when setting up the box is that the longest cutoff cannot exceed half the shortest box vector. If it does, you get duplicate force evaluations from a violation of the minimum image convention. Use of an NPT ensemble will cause the box dimensions to fluctuate (due to pressure) and thus it is unwise in such cases to ever have a box that is only twice the size of the longest cutoff, as violations are almost certain to occur. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Editing the functions of amber
Dear Matt Hopefully last question. Do you know if there's a way to get from replica exchange function energy of e certain group (like bonding energy)? It will make the implementation much easier. Thanks again, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Asaf Farhi [asaf.fa...@weizmann.ac.il] Sent: Thursday, March 22, 2012 6:00 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Editing the functions of amber Thank you very much. Have a nice weekend, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 5:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 2:56 AM, Asaf Farhi wrote: Thank you very much for the reply. I tried to send this question few days ago and they said that I'm not allowed to post there. (The edition of the replica exchange shouldn't be complicated.) Do you have any tips regarding what I should do? Read the RE documentation the manual and mdrun -h. Get out a debugger and step through the code. Most of the stuff relevant to replica exchange is in src/kernel/repl_ex.c Mark Thanks in advance, Best regards, Asaf_ ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 5:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 1:59 AM, Asaf Farhi wrote: Dear Matt Thank you very much for the reply. About 1 - it's cutoff in the energy, meaning that from a certain energy you will get this energy. Can this be done with the table lookups? Yes, any potential that is a function of distance between pairs can be done. See manual 6.7.2. Of course, plain cut-offs can be done without tables since about 1976... Are you willing to cooperate with us on 2? I don't have time for new projects, but a post to gmx-developers may elicit feedback on feasibility. Mark Thanks Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, March 22, 2012 4:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber On 23/03/2012 12:50 AM, Asaf Farhi wrote: Dear Matt Thank you very much for your reply. The things we want to change are the following: 1. Introduce a cutoff energy in the Van Der Waals and electrical potential. 2. Editing the replica exchange function. 3. Multiplying functions by a factor (mostly the covalent bond and constraints potentials). Probably you can do 1 and 3 with table lookups - see manual. Mark In the project we want to calculate free energy of RNAs. We want to run a MD simulation with these changes. We'll be happy to cooperate with you on this project (we hope that it'll lead to an article). Thank you very much, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Matthew Zwier [mczw...@gmail.com] Sent: Tuesday, March 20, 2012 8:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Editing the functions of amber Dear Asaf, I think we need significantly more information in order to help you. What function are you trying to port? What are you trying to do with it (that is, what is the scientific question you're trying to answer)? GROMACS is a clean codebase, and remarkably easy to read for how much computer science goes into it. However, there will likely be a relatively severe impedance mismatch between the AMBER and GROMACS code. AMBER is written primarily in FORTRAN, and GROMACS is written entirely in C. Data (like topology and coordinates) are stored differently in each code. Finally, GROMACS uses a lot of specialized techniques to speed up computations (table lookups instead of function calls, and the like), so implementing an algorithm in GROMACS is often more about re-expressing the algorithm in GROMACS style than it is about simply transliterating a routine from FORTRAN into C. What you're proposing is likely to be almost as formidable a task as implementing an algorithm from scratch based on the original papers. That said, our group has had success with modifying GROMACS code in the past, and it turned out to be an efficient solution. Cheers, Matt Zwier On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhiasaf.fa...@weizmann.ac.il wrote: Dear Gromacs User Hi. My name is Asaf and I'm trying to edit one of the functions in amber in order to use it in GROMACS. I wanted to ask if anyone knows how
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated
Hi Justin,
Thank you very much for all your time and help!
If you have time, can someone please help me understand how to read a .tpr
file? I convertied my .tpr file to human-readable form using gmxdump -s
topol.tpr.
Following an enumeration of all of the .mdp-like parameters, I see the
following section:
--
topology:
name=IL
#atoms = 6144
molblock (0):
moltype = 0 EMI
#molecules = 256
#atoms_mol = 19
#posres_xA = 0
#posres_xB = 0
molblock (1):
moltype = 1 BF4
#molecules = 256
#atoms_mol = 5
#posres_xA = 0
#posres_xB = 0
ffparams:
atnr=8
ntypes=100
functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
functype[1]=LJ_SR, c6= 2.60915095e-03, c12= 3.84019631e-06
functype[2]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
;...
functype[63]=LJ_SR, c6= 0.e+00, c12= 0.e+00
functype[64]=BONDS, b0A= 1.46600e-01, cbA= 2.82000e+05, b0B=
1.46600e-01, cbB= 2.82000e+05
;...
functype[70]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B=
1.08000e-01, cbB= 3.07106e+05
functype[71]=ANGLES, thA= 1.26400e+02, ctA= 5.85200e+02, thB=
1.26400e+02, ctB= 5.85200e+02
;...
functype[81]=ANGLES, thA= 1.12700e+02, ctA= 8.36800e+02, thB=
1.12700e+02, ctB= 8.36800e+02
functype[82]=RBDIHS, rbcA[0]= 1.9451e+01, rbcA[1]=
0.e+00, rbcA[2]=-1.9451e+01, rbcA[3]= 0.e+00, rbcA[4]=
0.e+00, rbcA[5]= 0.e+00
rbcB[0]= 1.9451e+01, rbcB[1]= 0.e+00, rbcB[2]=-1.9451e+01,
rbcB[3]= 0.e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00
;...
functype[88]=RBDIHS, rbcA[0]= 6.65499985e-01, rbcA[1]=
1.99650002e+00, rbcA[2]= 0.e+00, rbcA[3]=-2.6614e+00, rbcA[4]=
0.e+00, rbcA[5]= 0.e+00
rbcB[0]= 6.65499985e-01, rbcB[1]= 1.99650002e+00, rbcB[2]= 0.e+00,
rbcB[3]=-2.6614e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00
functype[89]=LJ14, c6A= 1.30457547e-03, c12A= 1.92009816e-06, c6B=
1.30457547e-03, c12B= 1.92009816e-06
;...
functype[97]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B=
6.12890653e-05, c12B= 1.49631507e-08
functype[98]=BONDS, b0A= 1.39300e-01, cbA= 2.42672e+05, b0B=
1.39300e-01, cbB= 2.42672e+05
functype[99]=ANGLES, thA= 1.09500e+02, ctA= 4.18400e+02, thB=
1.09500e+02, ctB= 4.18400e+02
reppow = 12
fudgeQQ = 0.5
--
My question is, how can I tell which atomtypes or pairs (I am not sure if
the indices refer to atomtypes or pairs) each functype[*]=LJ_SR, c6=*,
c12=* refers to? Each LJ_SR entry is indexed, but how do I determine what
the indices refer to?
In my .itp files which comprise my homemade force field, I define 22 unique
atomtypes, but here in the .tpr file, 63 LJ_SR entries are present. Does
this mean that the LJ_SR entries refer to pairs of atoms?
Later in the .tpr file, the residue types are listed, along with the atom
names. For example,
--
moltype (0):
name=EMI
atoms:
atom (19):
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m=
1.40067e+01, q= 1.5e-01, mB= 1.40067e+01, qB= 1.5e-01, resind=0,
atomnumber= 7}
;...
atom[18]={type= 3, typeB= 3, ptype=Atom, m=
1.00790e+00, q= 6.0e-02, mB= 1.00790e+00, qB= 6.0e-02, resind=0,
atomnumber= 1}
atom (19):
atom[0]={name=NA}
;...
atom[18]={name=HC}
type (19):
type[0]={name=NA,nameB=NA}
;...
type[18]={name=HC,nameB=HC}
residue (1):
residue[0]={name=EMI, nr=1, ic=' '}
cgs:
nr=13
cgs[0]={0..1}
;...
cgs[12]={16..18}
excls:
nr=19
nra=195
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13}
;...
excls[18][187..194]={1, 6, 7, 14, 15, 16, 17, 18}
Bond:
nr: 57
iatoms:
0 type=64 (BONDS) 0 2
;...
18 type=69 (BONDS) 7 18
Angle:
nr: 132
iatoms:
0 type=71 (ANGLES) 2 0 3
;...
32 type=75 (ANGLES) 17 7 18
Ryckaert-Bell.:
nr: 165
iatoms:
0 type=82 (RBDIHS) 0 3 1 5
;...
32 type=88 (RBDIHS) 15 6 7 18
LJ-14:
nr: 108
iatoms:
0 type=89 (LJ14) 0 6
;...
35 type=97 (LJ14) 15 18
--
and similarly for the other residues. But, I do not see LJ_SR entries in
these residue sections. So, how can I determine what the LJ_SR entries are
[gmx-users] Re: quasi-harmonic entropy calculation
My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl script, but when I compare the entropy calculated through both methods for my entire protein the results diverges in one order of magnitud and I give to the script the same eigenvalues obtained by g_covar (g_anaeig uses the eigenvectors). Please, help me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_wham position 0
Hi all, I am experiencing a potential problem with my PMF curve not starting at position 0 of the reaction coordinate, which is defined by a path starting from 0.0 nm and ending at 0.5 nm. When I run the GROMACS g_wham analysis at Umb. Pos 0.0 (see below), to say, 0.02 nm, the PMF curve doesn't start out at 0.0 nm but gets offset to ~0.01 nm in the resulting figure. Its corresponding histogram also gets offset by the same amount. This is particularly peculiar to me because my frame1 *is* the structure at 0.0nm of the S path. I also double-checked my COLVAR file and there are no negative values in my COLVAR file: # UMBRELLA3.0 # Compnent selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 1 # Group 1 'GR1' Umb. Pos. 0.0 Umb. Cons. 5 # 0.0300 0.47500 0.0400 0.000103337 0.0500 0.000163820 0.0600 0.000265547 0.0700 0.000408777 0.0800 0.000550200 0.0900 0.000653522 Has anyone else experienced this problem before? I'm hoping it's just some minor issue in g_wham. I even invoked the -zprof0 flag to - zprof 0 and it did not set my PMF curve to start at 0. Sincerely, Lili -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated
Andrew DeYoung wrote:
Hi Justin,
Thank you very much for all your time and help!
If you have time, can someone please help me understand how to read a .tpr
file? I convertied my .tpr file to human-readable form using gmxdump -s
topol.tpr.
Following an enumeration of all of the .mdp-like parameters, I see the
following section:
--
topology:
name=IL
#atoms = 6144
molblock (0):
moltype = 0 EMI
#molecules = 256
#atoms_mol = 19
#posres_xA = 0
#posres_xB = 0
molblock (1):
moltype = 1 BF4
#molecules = 256
#atoms_mol = 5
#posres_xA = 0
#posres_xB = 0
ffparams:
atnr=8
ntypes=100
functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
functype[1]=LJ_SR, c6= 2.60915095e-03, c12= 3.84019631e-06
functype[2]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
;...
functype[63]=LJ_SR, c6= 0.e+00, c12= 0.e+00
functype[64]=BONDS, b0A= 1.46600e-01, cbA= 2.82000e+05, b0B=
1.46600e-01, cbB= 2.82000e+05
;...
functype[70]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B=
1.08000e-01, cbB= 3.07106e+05
functype[71]=ANGLES, thA= 1.26400e+02, ctA= 5.85200e+02, thB=
1.26400e+02, ctB= 5.85200e+02
;...
functype[81]=ANGLES, thA= 1.12700e+02, ctA= 8.36800e+02, thB=
1.12700e+02, ctB= 8.36800e+02
functype[82]=RBDIHS, rbcA[0]= 1.9451e+01, rbcA[1]=
0.e+00, rbcA[2]=-1.9451e+01, rbcA[3]= 0.e+00, rbcA[4]=
0.e+00, rbcA[5]= 0.e+00
rbcB[0]= 1.9451e+01, rbcB[1]= 0.e+00, rbcB[2]=-1.9451e+01,
rbcB[3]= 0.e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00
;...
functype[88]=RBDIHS, rbcA[0]= 6.65499985e-01, rbcA[1]=
1.99650002e+00, rbcA[2]= 0.e+00, rbcA[3]=-2.6614e+00, rbcA[4]=
0.e+00, rbcA[5]= 0.e+00
rbcB[0]= 6.65499985e-01, rbcB[1]= 1.99650002e+00, rbcB[2]= 0.e+00,
rbcB[3]=-2.6614e+00, rbcB[4]= 0.e+00, rbcB[5]= 0.e+00
functype[89]=LJ14, c6A= 1.30457547e-03, c12A= 1.92009816e-06, c6B=
1.30457547e-03, c12B= 1.92009816e-06
;...
functype[97]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B=
6.12890653e-05, c12B= 1.49631507e-08
functype[98]=BONDS, b0A= 1.39300e-01, cbA= 2.42672e+05, b0B=
1.39300e-01, cbB= 2.42672e+05
functype[99]=ANGLES, thA= 1.09500e+02, ctA= 4.18400e+02, thB=
1.09500e+02, ctB= 4.18400e+02
reppow = 12
fudgeQQ = 0.5
--
My question is, how can I tell which atomtypes or pairs (I am not sure if
the indices refer to atomtypes or pairs) each functype[*]=LJ_SR, c6=*,
c12=* refers to? Each LJ_SR entry is indexed, but how do I determine what
the indices refer to?
In my .itp files which comprise my homemade force field, I define 22 unique
atomtypes, but here in the .tpr file, 63 LJ_SR entries are present. Does
this mean that the LJ_SR entries refer to pairs of atoms?
I haven't dissected this information for a while, but here's my understanding.
Someone please correct me if I'm wrong. The list contains all the function
types that are used in the simulation, with each assigned an index. What you're
interested in are the LJ_SR parameters, which are constructed (again, this is
just my interpretation from systems that I have used) by stepping through all of
the atoms in each molecule and adding a new function when it is needed. That
is, for a simple protein using Gromos96 53A6, the first few lines are (my
comments added after ';'):
functype[0]=LJ_SR, c6= 2.43640970e-03, c12= 2.31952890e-06 ; NL-NL
functype[1]=LJ_SR, c6= 0.e+00, c12= 0.e+00 ; H-NL
functype[2]=LJ_SR, c6= 3.84514406e-03, c12= 1.50015503e-05 ; CH1-NL
functype[3]=LJ_SR, c6= 4.26569115e-03, c12= 8.87604438e-06 ; CH2-NL
Thus it is stepping through each new atomtype (mapped to N, H, C-alpha, C-beta,
etc) in the amino acid and generating parameters for interactions between itself
and all prior atomtypes that have been encountered. You can check in the
[nonbond_params] directive to see where some special values are used. For
Gromos96, NL-NL interactions have no special values to them, the normal C6/C12
parameters are used. This is not, however, the case for other atomtypes, where
special combinations are used.
Later in the .tpr file, the residue types are listed, along with the atom
names. For example,
--
moltype (0):
name=EMI
atoms:
atom (19):
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m=
1.40067e+01, q= 1.5e-01, mB= 1.40067e+01, qB= 1.5e-01, resind=0,
atomnumber= 7}
;...
[gmx-users] radial distribution normal in g_order
Can someone explain to me what compute a radial membrane normal means in the g_order options. I would like to calculate S with respect to the surface of a spherical particle instead of one of the axes. Is this what it does? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated
Justin, Thanks. So I imagine that the order that the atoms are stepped through is dictated by the order of atoms in the configuration file (.gro or .pdb); do you think that this is correct? I am not simulating a protein, so other than the order of atoms in the configuration file, for my system there is not any obvious order to use (such as N terminus, H attached to N terminus, C-alpha, etc). Thanks! Andrew DeYoung Carnegie Mellon University I haven't dissected this information for a while, but here's my understanding. Someone please correct me if I'm wrong. The list contains all the function types that are used in the simulation, with each assigned an index. What you're interested in are the LJ_SR parameters, which are constructed (again, this is just my interpretation from systems that I have used) by stepping through all of the atoms in each molecule and adding a new function when it is needed. That is, for a simple protein using Gromos96 53A6, the first few lines are (my comments added after ';'): functype[0]=LJ_SR, c6= 2.43640970e-03, c12= 2.31952890e-06 ; NL-NL functype[1]=LJ_SR, c6= 0.e+00, c12= 0.e+00 ; H-NL functype[2]=LJ_SR, c6= 3.84514406e-03, c12= 1.50015503e-05 ; CH1-NL functype[3]=LJ_SR, c6= 4.26569115e-03, c12= 8.87604438e-06 ; CH2-NL Thus it is stepping through each new atomtype (mapped to N, H, C-alpha, C-beta, etc) in the amino acid and generating parameters for interactions between itself and all prior atomtypes that have been encountered. You can check in the [nonbond_params] directive to see where some special values are used. For Gromos96, NL-NL interactions have no special values to them, the normal C6/C12 parameters are used. This is not, however, the case for other atomtypes, where special combinations are used. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated
Andrew DeYoung wrote: Justin, Thanks. So I imagine that the order that the atoms are stepped through is dictated by the order of atoms in the configuration file (.gro or .pdb); do you think that this is correct? I am not simulating a protein, so other than the order of atoms in the configuration file, for my system there is not any obvious order to use (such as N terminus, H attached to N terminus, C-alpha, etc). Yes, from everything I can tell the order that is used is the one found in the coordinate file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: quasi-harmonic entropy calculation
Op 22 mar 2012 om 15:27 heeft wmira...@estudiantes.fbio.uh.cu het volgende geschreven: My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl script, but when I compare the entropy calculated through both methods for my entire protein the results diverges in one order of magnitud and I give to the script the same eigenvalues obtained by g_covar (g_anaeig uses the eigenvectors). Please, help me. Thanks Is there readon to assume g_anaeig is incorrect? There is numerical problem with this calculation due to the large range of numbers and therefore the g_anaeig program uses ligarithms. Please compare the source code in case of doubt. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: quasi-harmonic entropy calculation
Hi, IIRC I tested g_anaeig when David wrote it and the results were the same as calc_entropies.pl, so it sounds strange. Are you sure you use the same input in both cases? Did you use the eigenvectors that correspond to the same eigenvalues? Also, how may eigenvalues are close to zero? Ran Message: 4 Date: Thu, 22 Mar 2012 10:27:36 -0400 From: wmira...@estudiantes.fbio.uh.cu Subject: [gmx-users] Re: quasi-harmonic entropy calculation To: gmx-users@gromacs.org Message-ID: 5e667c140e0c268c9e87681be3535b89.squir...@est.fbio.uh.cu Content-Type: text/plain;charset=iso-8859-1 My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl script, but when I compare the entropy calculated through both methods for my entire protein the results diverges in one order of magnitud and I give to the script the same eigenvalues obtained by g_covar (g_anaeig uses the eigenvectors). Please, help me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] submision
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
