Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield
Hello Users, I am running mdrun for nsteps = 1000 ; 20 ns. Even though i have enough space on my cluster around 17 GB, I am getting the following error. *Cannot fsync 'md1.log'; maybe you are out of disk space?* What could be the reason for such errors. I am attaching my mdp file. Thanks in Advance. On Wed, Feb 26, 2014 at 6:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/26/14, 7:05 AM, lalithkumar wrote: Dear Dr. Justin, Thank you for pointing out the details of error. I have missed out the version of GROMACS I have been using and so I would like to let you know that my version is 4.5.7. In this version ffnonbonded.itp file of the gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I I doubt that's correct; every Gromacs version I've ever had contained [pairtypes] in this file. Check again. I don't have 4.5.7 installed anywhere, but in 4.6.x (several versions), it is clearly present. should agree that I dont know how they can be generated and to specify manually. So, in a crude way I can say that I have copied all the LJ 14 types from the ffG43a1p forcefield at the gromacs contributors link: http://www.gromacs.org/Downloads/User_contributions/Force_fields This includes the following addition lines: ; begin insert from pamac_hsnnb.itp ; [ pairtypes ] ; for LJ 14 - use same for OP as for OA OPO 1 0.0022619536 9.687375e-07 OP OM 1 0.0022619536 9.687375e-07 OP OP 1 0.0022619536 1.265625e-06 OW OP 1 0.0024331696 1.737e-06 N OP 1 0.0023475616 1.463625e-06 NT OP 1 0.0023475616 1.463625e-06 NL OP 1 0.0023475616 1.463625e-06 NR OP 1 0.0023475616 1.463625e-06 NZ OP 1 0.0023475616 1.463625e-06 NE OP 1 0.0023475616 1.463625e-06 C OP 1 0.0023009528 2.066625e-06 CH1 OP 1 0.0025663376 2.174625e-06 CH2 OP 1 0.0032687988 3.000375e-06 CH3 OP 1 0.0039370168 3.907125e-06 CH4 OP 1 0.005459888 6.59475e-06 CR1 OP 1 0.003536086 3.24675e-06 HC OP 1 0.000437552 1.38375e-07 H OP 1 0 0 DUM OP 1 0 0 S OP 1 0.0047521952 4.068e-06 CU1+ OP 1 0.000972602 8.053875e-08 CU2+ OP 1 0.000972602 8.053875e-08 FE OP 1 0 0 ZN2+ OP 1 0.000972602 1.09305e-07 MG2+ OP 1 0.0003842848 6.56775e-08 CA2+ OP 1 0.001507652 7.939125e-07 P OP 1 0.005773784 5.299875e-06 AR OP 1 0.003764374 3.53025e-06 F OP 1 0.0016322592 9.81225e-07 CL OP 1 0.0044525672 4.399875e-06 BR OP 1 0.0016332104 9.1035e-06 CMET OP 1 0.0044806276 5.1373125e-06 OMET OP 1 0.0022619536 1.265625e-06 NA+ OP 1 0.00040373684 1.63125e-07 CL- OP 1 0.0055883 1.16325e-05 CCHL OP 1 0.0024394475 2.268e-06 CLCHL OP 1 0.004334666 4.1738625e-06 HCHL OP 1 0.0002920184 7.377075e-08 SDMSO OP 1 0.0048877412 5.216175e-06 CDMSO OP 1 0.0045248108 5.2475625e-06 ODMSO OP 1 0.0022663291 9.752175e-07 CCL4 OP 1 0.0024394475 3.1014e-06 CLCL4 OP 1 0.0041472796 4.01985e-06 SI OP 1 0 0 ; end insert from pamac_hsnnb.itp And I had copied them as is to my ffnonbonded.itp file in modified gromos53a6.ff folder. Also, I have also modified atomtypes as per latest versions (for example CMET to CMet). Finally, I could pass the grompp set now and can run mdrun too successfully. Now I need your valuable review to know whether I had done is correct or can I do better than this way. If so please suggest some helping material regarding process of setting user defined LJ 14 pair types interactions to gromos53a6ff or any forcefield. And also, briefly comment on how difference with my results by doing in the method mentioned by me and with any other suggested method from your side. Please let me know if any further information to be provided from my side What you've done is not correct. You've made a mixed force field that is not necessarily viable. You need proper parameters within a single force field, not borrowed from some other parameter set, unless you can demonstrate through rigorous testing and validation that what you've done is correct. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201
Re: [gmx-users] Launching MPI/OpenMP hybrid run
On 04 Mar 2014, at 13:08, Alexander Björling alex.bjorl...@gmail.com wrote: Dear users, I'm trying to run simulations on a cluster of nodes, each sporting two AMD Opteron 8-core CPU:s. I would like to have one MPI process on each CPU, with OpenMP threads on the 8 cores of each. I've compiled gromacs 5.0 with intel MPI and OpenMP enabled. To get it running I'm just using two nodes, so 4 MPI processes. I've been using various combinations of the type: mpirun -np 4 -perhost 2 gmx_mpi mdrun -ntomp 8 ..., but I never manage to get the MPI process spread out on the two nodes. Rather, in the example above, 4 MPI processes with 4 OpenMP threads each runs on the first node, and the second node does nothing. Did you provide a hostfile / machinefile containing the names of your nodes you want the MPI processes to be started on? Carsten Any hints would be most appreciated, Cheers, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Launching MPI/OpenMP hybrid run
Carsten Kutzner wrote On 04 Mar 2014, at 13:08, Alexander Björling lt; alex.bjorling@ gt; wrote: Dear users, I'm trying to run simulations on a cluster of nodes, each sporting two AMD Opteron 8-core CPU:s. I would like to have one MPI process on each CPU, with OpenMP threads on the 8 cores of each. I've compiled gromacs 5.0 with intel MPI and OpenMP enabled. To get it running I'm just using two nodes, so 4 MPI processes. I've been using various combinations of the type: mpirun -np 4 -perhost 2 gmx_mpi mdrun -ntomp 8 ..., but I never manage to get the MPI process spread out on the two nodes. Rather, in the example above, 4 MPI processes with 4 OpenMP threads each runs on the first node, and the second node does nothing. Did you provide a hostfile / machinefile containing the names of your nodes you want the MPI processes to be started on? No, I just asked SLURM for two nodes, the way I would if I was running MPI-only jobs. -- View this message in context: http://gromacs.5086.x6.nabble.com/Launching-MPI-OpenMP-hybrid-run-tp5014934p5014936.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Launching MPI/OpenMP hybrid run
On 04 Mar 2014, at 13:43, alex.bjorling alex.bjorl...@gmail.com wrote: Carsten Kutzner wrote On 04 Mar 2014, at 13:08, Alexander Björling lt; alex.bjorling@ gt; wrote: Dear users, I'm trying to run simulations on a cluster of nodes, each sporting two AMD Opteron 8-core CPU:s. I would like to have one MPI process on each CPU, with OpenMP threads on the 8 cores of each. I've compiled gromacs 5.0 with intel MPI and OpenMP enabled. To get it running I'm just using two nodes, so 4 MPI processes. I've been using various combinations of the type: mpirun -np 4 -perhost 2 gmx_mpi mdrun -ntomp 8 ..., but I never manage to get the MPI process spread out on the two nodes. Rather, in the example above, 4 MPI processes with 4 OpenMP threads each runs on the first node, and the second node does nothing. Did you provide a hostfile / machinefile containing the names of your nodes you want the MPI processes to be started on? No, I just asked SLURM for two nodes, the way I would if I was running MPI-only jobs. Then SLURM is not positioning your MPI processes correctly. This problem should be independent of Gromacs. Carsten -- View this message in context: http://gromacs.5086.x6.nabble.com/Launching-MPI-OpenMP-hybrid-run-tp5014934p5014936.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Out of Disk Space
Hi everybody, I am running mdrun_mpi V 4.6.5 for nsteps=1000; 20 ns My simulation is getting stopped at 500ps and I am getting following error even though i have enough space on my cluster around 17 GB. *Cannot fsync 'md1.trr'; maybe you are out of disk space?* *Cannot fsync 'md1.log'; maybe you are out of disk space?* I have executed for two times, each time i get different error. What is the reason for the above error. I am sharing my mdp file. Any help is appreciated. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- 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] Out of Disk Space
Hi Pavan, When you use the grompp command to prepare the md.tpr file for the final mdrun, do you notice such a statement This run will generate roughly X Mb of data. I suspect the resultant trajectory could be exceeding the available space. On Tue, Mar 4, 2014 at 4:12 PM, Pavan Kumar kumar.pavan...@gmail.comwrote: Hi everybody, I am running mdrun_mpi V 4.6.5 for nsteps=1000; 20 ns My simulation is getting stopped at 500ps and I am getting following error even though i have enough space on my cluster around 17 GB. *Cannot fsync 'md1.trr'; maybe you are out of disk space?* *Cannot fsync 'md1.log'; maybe you are out of disk space?* I have executed for two times, each time i get different error. What is the reason for the above error. I am sharing my mdp file. Any help is appreciated. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Out of Disk Space
It could be a quota issue (there is free space, but your group has used its entire allocation). Also, file systems often have limits not only on the total amount of space, but also on the total number of files that a group is allowed to create. Talk to your system administrator. There is likely a special command that you can run to find the relevant information (e.g., quota, diskUsage, prquota, etc... these are usually scripts written by your administrators so the name could in theory be anything). Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Pavan Kumar kumar.pavan...@gmail.com Sent: 04 March 2014 09:38 To: gmx-users Subject: Re: [gmx-users] Out of Disk Space Hello THOMMAS, Exactly, it showed 2.2GB of trajectory is going to be created. But i have 17GB of free space on my cluster on which i am running. So any other reasons for the error. Thanks in advance. On Tue, Mar 4, 2014 at 8:00 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Hi Pavan, When you use the grompp command to prepare the md.tpr file for the final mdrun, do you notice such a statement This run will generate roughly X Mb of data. I suspect the resultant trajectory could be exceeding the available space. On Tue, Mar 4, 2014 at 4:12 PM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hi everybody, I am running mdrun_mpi V 4.6.5 for nsteps=1000; 20 ns My simulation is getting stopped at 500ps and I am getting following error even though i have enough space on my cluster around 17 GB. *Cannot fsync 'md1.trr'; maybe you are out of disk space?* *Cannot fsync 'md1.log'; maybe you are out of disk space?* I have executed for two times, each time i get different error. What is the reason for the above error. I am sharing my mdp file. Any help is appreciated. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- 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. -- Thanks Regards, Pavan Kumar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)
Done: http://redmine.gromacs.org/issues/1449
João
On Tue, Mar 4, 2014 at 6:56 AM, David van der Spoel sp...@xray.bmc.uu.sewrote:
On 2014-03-04 04:39, João M. Damas wrote:
Hello Teemu,
Thank you! I am glad the GROMACS team is concerned about this particular
problem.
And I am sorry for my late reply.
For the sake of conciseness, so we do not get lost in the data, I am only
showing the single precision results (we may bring double precision later
on again). Also, since GROMACS 4.0.4 is flawed in the -pbc flag, as Teemu
said, I also excluded it from these results (it is not going to get
corrected anyway).
I compiled a GROMACS version 4.6.3 with the fix presented in
https://gerrit.gromacs.org/#/c/3199/ (in single precision).
I repeated the tests and the results are presented in Attached Table 3.
- the fix brings the -nopbc results close (within 1 square angstrom)
to
the ones obtained by ASC, except for 1TIM where the difference is
within
10-20 square angstrom. Maybe 1TIM has a difficult shape, because ASC
also
had the largest difference between numerical DCLM and the analytical
method
in this protein.
- the -pbc yes results though, do not change (which is normal,
considering the flag is working in this version and the fix is inside
a
conditional expression that depends on the -pbc flag). It continues to
baffle me why this is happening. If the molecule is inside the box
and far
from the edges (again, a test using a .gro created by editconf -d 5
gave
the same exact table as Attached Table 3), I see no reason why these
results should be different...
So, I think Bug #1445 http://redmine.gromacs.org/issues/1445 is indeed
solved, but we still need to solve an unknown bug with -pbc yes. Should
I
open a new bug related to this in the redmine?
In short, yes. If the protein is in the center of the box with no periodic
contacts the result should be the same as without pbc.
I can perform more tests, if anyone has more ideas.
Best,
João
--
Attached Table 3
met - method used, anl=analytical method, num=numerical method (DCLM)
dots - number of points used for the numerical method
src - source of the data, paper=Eisenhaber1995, ASC=ASC software,
g463{sp,fx}=g_sas of GMX4.6.3 {single precision,fix
3199https://gerrit.gromacs.org/#/c/3199/
}
pbc - PBC flag for g_sas, yes=-pbc, no=-nopbc
Areas are in square angstrom
==
met dots src pbc 4PTI 3FXN 1TIM
==
anl paper3973.80 6943.80 20002.80
anl ASC3973.81 6943.80 20002.80
num 122 paper3961.40 6968.30 19970.90
num 122 ASC3961.44 6968.33 19970.90
num 122 g463sp yes 3825.86 6257.83 19867.90
num 122 g463sp no 4169.21 7731.63 24080.20
num 122 g463fx yes 3825.86 6257.83 19867.90
num 122 g463fx no 3957.81 6955.99 20004.20
num 362 paper3971.80 6933.40 19997.10
num 362 ASC3971.79 6933.37 19997.10
num 362 g463sp yes 3838.35 6248.43 19886.80
num 362 g463sp no 4195.02 7704.70 24132.10
num 362 g463fx yes 3838.35 6248.43 19886.80
num 362 g463fx no 3969.92 6936.20 20016.70
num 642 paper3967.90 6944.40 19998.70
num 642 ASC3967.78 6944.37 19998.70
num 642 g463sp yes 3831.64 6255.64 19882.70
num 642 g463sp no 4188.63 7701.99 24119.40
num 642 g463fx yes 3831.64 6255.64 19882.70
num 642 g463fx no 3966.21 6941.26 20013.60
num 1002 paper3974.10 6939.10 20012.20
num 1002 ASC3974.07 6939.12 20012.20
num 1002 g463sp yes 3840.58 6250.14 19897.40
num 1002 g463sp no 4193.60 7700.64 24143.10
num 1002 g463fx yes 3840.58 6250.14 19897.40
num 1002 g463fx no 3973.51 6939.68 20027.50
num 1472 paper3975.70 6943.30 19997.00
num 1472 ASC3975.70 6943.35 19996.90
num 1472 g463sp yes 3841.69 6256.92 19882.80
num 1472 g463sp no 4198.08 7709.30 24123.30
num 1472 g463fx yes 3841.69 6256.92 19882.80
num 1472 g463fx no 3975.88 6943.96 20012.40
==
On Fri, Feb 28, 2014 at 4:49 AM, Teemu Murtola teemu.murt...@gmail.com
wrote:
Hi,
On Thu, Feb 27, 2014 at 4:09 PM, Teemu Murtola teemu.murt...@gmail.com
wrote:
I'll post additional information once I have had time to test more
cases.
I have now created http://redmine.gromacs.org/issues/1445 to track the
issue, and uploaded a fix to Gerrit: https://gerrit.gromacs.org/#/
c/3199/
.
My current set of tests is here: https://gerrit.gromacs.org/#/c/3200/
Re: [gmx-users] Out of Disk Space
I have executed for two times, each time i get different error. And you got *different* errors... What's the difference? Did you get the error at exactly the same integration time-step? Did you try to resproduce the error on another disk partition? Dr. Vitaly V. Chaban -- 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] REMD Melting Curve
Dear Sir, I successfully ran demix.pl and generated the xvg files - replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as melt.xvg below .. # This file was created Wed Feb 26 10:10:27 2014 # by the following command: # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg # # g_kinetics_d is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @ title Melting curve @ xaxis label T (K) @ yaxis label @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Folded fraction @ s1 legend DG (kJ/mole) 260 0.929 5.556 261 0.927 5.500 262 0.924 5.445 263 0.922 5.389 264 0.919 5.334 265 0.916 5.278 266 0.914 5.223 267 0.911 5.167 268 0.908 5.112 269 0.906 5.056 270 0.903 5.000 271 0.900 4.945 272 0.897 4.889 273 0.894 4.834 274 0.891 4.778 275 0.888 4.723 276 0.884 4.667 277 0.881 4.612 278 0.878 4.556 279 0.874 4.500 280 0.871 4.445 281 0.867 4.389 282 0.864 4.334 283 0.860 4.278 284 0.857 4.223 285 0.853 4.167 286 0.849 4.112 287 0.845 4.056 288 0.842 4.000 289 0.838 3.945 290 0.834 3.889 291 0.830 3.834 292 0.826 3.778 293 0.822 3.723 294 0.818 3.667 295 0.813 3.612 296 0.809 3.556 297 0.805 3.500 298 0.801 3.445 299 0.796 3.389 300 0.792 3.334 301 0.787 3.278 302 0.783 3.223 303 0.779 3.167 304 0.774 3.112 305 0.769 3.056 306 0.765 3.000 307 0.760 2.945 308 0.756 2.889 309 0.751 2.834 310 0.746 2.778 311 0.741 2.723 312 0.737 2.667 313 0.732 2.612 314 0.727 2.556 315 0.722 2.500 316 0.717 2.445 317 0.712 2.389 318 0.707 2.334 319 0.702 2.278 320 0.697 2.223 321 0.693 2.167 322 0.688 2.112 323 0.683 2.056 324 0.678 2.001 325 0.673 1.945 326 0.668 1.889 327 0.663 1.834 328 0.657 1.778 329 0.652 1.723 330 0.647 1.667 331 0.642 1.612 332 0.637 1.556 333 0.632 1.501 334 0.627 1.445 335 0.622 1.389 336 0.617 1.334 337 0.612 1.278 338 0.607 1.223 339 0.602 1.167 340 0.597 1.112 341 0.592 1.056 342 0.587 1.001 343 0.582 0.945 344 0.577 0.889 345 0.572 0.834 346 0.567 0.778 347 0.562 0.723 348 0.557 0.667 349 0.553 0.612 350 0.548 0.556 351 0.543 0.501 352 0.538 0.445 353 0.533 0.389 354 0.528 0.334 355 0.524 0.278 356 0.519 0.223 357 0.514 0.167 358 0.509 0.112 359 0.505 0.056 360 0.500 0.001 361 0.495 -0.055 362 0.491 -0.111 363 0.486 -0.166 364 0.482 -0.222 365 0.477 -0.277 366 0.473 -0.333 367 0.468 -0.388 368 0.464 -0.444 369 0.459 -0.499 370 0.455 -0.555 371 0.451 -0.611 372 0.446 -0.666 373 0.442 -0.722 374 0.438 -0.777 375 0.434 -0.833 376 0.429 -0.888 377 0.425 -0.944 378 0.421 -0.999 379 0.417 -1.055 380 0.413 -1.111 381 0.409 -1.166 382 0.405 -1.222 383 0.401 -1.277 384 0.397 -1.333 385 0.393 -1.388 386 0.389 -1.444 387 0.386 -1.499 388 0.382 -1.555 389 0.378 -1.610 390 0.374 -1.666 391 0.371 -1.722 392 0.367 -1.777 393 0.363 -1.833 394 0.360 -1.888 395 0.356 -1.944 396 0.353 -1.999 397 0.349 -2.055 398 0.346 -2.110 399 0.342 -2.166 400 0.339 -2.222 401 0.336 -2.277 402 0.332 -2.333 403 0.329 -2.388 404 0.326 -2.444 405 0.323 -2.499 406 0.319 -2.555 407 0.316 -2.610 408 0.313 -2.666 409 0.310 -2.722 410 0.307 -2.777 411 0.304 -2.833 412 0.301 -2.888 413 0.298 -2.944 414 0.295 -2.999 415 0.292 -3.055 416 0.289 -3.110 417 0.286 -3.166 418 0.284 -3.222 419 0.281 -3.277 420 0.278 -3.333 So, as you can see, I got folded fraction and associated free energy change at each temperature ranging from 260-420K. Atanu On Tuesday, 4 March 2014
Re: [gmx-users] Launching MPI/OpenMP hybrid run
On Tue, Mar 4, 2014 at 1:08 PM, Alexander Björling alex.bjorl...@gmail.comwrote: Dear users, I'm trying to run simulations on a cluster of nodes, each sporting two AMD Opteron 8-core CPU:s. I would like to have one MPI process on each CPU, with OpenMP threads on the 8 cores of each. I've compiled gromacs 5.0 with intel MPI and OpenMP enabled. To get it running I'm just using two nodes, so 4 MPI processes. I've been using various combinations of the type: mpirun -np 4 -perhost 2 gmx_mpi mdrun -ntomp 8 ..., but I never manage to get the MPI process spread out on the two nodes. Rather, in the example above, 4 MPI processes with 4 OpenMP threads each runs on the first node, and the second node does nothing. mdrun will just work with whatever the MPI environment says exists, so I would look to your mpirun docs to find out what you should do. Mark Any hints would be most appreciated, Cheers, Alex -- 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] access to gmx
Dear gmx users I installed fftw and gromacs 4.5.3 version under home directory (both double-precision), after installation I tried the following commands but none of them could introduce gromacs to the bash shell: 1.make links 2.source /home/WeNMR/ProgramFiles/gromacs/bin/GMXRC, GMXRC.bash or GMXRC.* 3.export PATH=$PATH:/home/WeNMR/ProgramFiles/gromacs/bin in basrc To be assure of correct instaIlation, I run one of the programs e.g. pdb2gmx by the following command in /home/WeNMR/ProgramFiles/gromacs/bin directory: ./bdb2gmx_d How could I get access to gromacs? Sincerely M.Javaheri -- 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] REMD Melting Curve
On 3/4/14, 12:22 PM, atanu das wrote: Dear Sir, I successfully ran demix.pl and generated the xvg files - replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as melt.xvg below .. # This file was created Wed Feb 26 10:10:27 2014 # by the following command: # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg # # g_kinetics_d is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @title Melting curve @xaxis label T (K) @yaxis label @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Folded fraction @ s1 legend DG (kJ/mole) 260 0.929 5.556 261 0.927 5.500 262 0.924 5.445 263 0.922 5.389 264 0.919 5.334 265 0.916 5.278 266 0.914 5.223 267 0.911 5.167 268 0.908 5.112 269 0.906 5.056 270 0.903 5.000 271 0.900 4.945 272 0.897 4.889 273 0.894 4.834 274 0.891 4.778 275 0.888 4.723 276 0.884 4.667 277 0.881 4.612 278 0.878 4.556 279 0.874 4.500 280 0.871 4.445 281 0.867 4.389 282 0.864 4.334 283 0.860 4.278 284 0.857 4.223 285 0.853 4.167 286 0.849 4.112 287 0.845 4.056 288 0.842 4.000 289 0.838 3.945 290 0.834 3.889 291 0.830 3.834 292 0.826 3.778 293 0.822 3.723 294 0.818 3.667 295 0.813 3.612 296 0.809 3.556 297 0.805 3.500 298 0.801 3.445 299 0.796 3.389 300 0.792 3.334 301 0.787 3.278 302 0.783 3.223 303 0.779 3.167 304 0.774 3.112 305 0.769 3.056 306 0.765 3.000 307 0.760 2.945 308 0.756 2.889 309 0.751 2.834 310 0.746 2.778 311 0.741 2.723 312 0.737 2.667 313 0.732 2.612 314 0.727 2.556 315 0.722 2.500 316 0.717 2.445 317 0.712 2.389 318 0.707 2.334 319 0.702 2.278 320 0.697 2.223 321 0.693 2.167 322 0.688 2.112 323 0.683 2.056 324 0.678 2.001 325 0.673 1.945 326 0.668 1.889 327 0.663 1.834 328 0.657 1.778 329 0.652 1.723 330 0.647 1.667 331 0.642 1.612 332 0.637 1.556 333 0.632 1.501 334 0.627 1.445 335 0.622 1.389 336 0.617 1.334 337 0.612 1.278 338 0.607 1.223 339 0.602 1.167 340 0.597 1.112 341 0.592 1.056 342 0.587 1.001 343 0.582 0.945 344 0.577 0.889 345 0.572 0.834 346 0.567 0.778 347 0.562 0.723 348 0.557 0.667 349 0.553 0.612 350 0.548 0.556 351 0.543 0.501 352 0.538 0.445 353 0.533 0.389 354 0.528 0.334 355 0.524 0.278 356 0.519 0.223 357 0.514 0.167 358 0.509 0.112 359 0.505 0.056 360 0.500 0.001 361 0.495-0.055 362 0.491-0.111 363 0.486-0.166 364 0.482-0.222 365 0.477-0.277 366 0.473-0.333 367 0.468-0.388 368 0.464-0.444 369 0.459-0.499 370 0.455-0.555 371 0.451-0.611 372 0.446-0.666 373 0.442-0.722 374 0.438-0.777 375 0.434-0.833 376 0.429-0.888 377 0.425-0.944 378 0.421-0.999 379 0.417-1.055 380 0.413-1.111 381 0.409-1.166 382 0.405-1.222 383 0.401-1.277 384 0.397-1.333 385 0.393-1.388 386 0.389-1.444 387 0.386-1.499 388 0.382-1.555 389 0.378-1.610 390 0.374-1.666 391 0.371-1.722 392 0.367-1.777 393 0.363-1.833 394 0.360-1.888 395 0.356-1.944 396 0.353-1.999 397 0.349-2.055 398 0.346-2.110 399 0.342-2.166 400 0.339-2.222 401 0.336-2.277 402 0.332-2.333 403 0.329-2.388 404 0.326-2.444 405 0.323-2.499 406 0.319-2.555 407 0.316-2.610 408 0.313-2.666 409 0.310-2.722 410 0.307-2.777 411 0.304-2.833 412 0.301-2.888 413 0.298-2.944 414 0.295-2.999 415 0.292-3.055 416 0.289-3.110 417 0.286-3.166 418 0.284-3.222 419
Re: [gmx-users] access to gmx
On 3/4/14, 4:32 PM, Mostafa Javaheri wrote: Dear gmx users I installed fftw and gromacs 4.5.3 version under home directory (both double-precision), after installation I tried the following commands but none of them could introduce gromacs to the bash shell: 1.make links 2.source /home/WeNMR/ProgramFiles/gromacs/bin/GMXRC, GMXRC.bash or GMXRC.* 3.export PATH=$PATH:/home/WeNMR/ProgramFiles/gromacs/bin in basrc To be assure of correct instaIlation, I run one of the programs e.g. pdb2gmx by the following command in /home/WeNMR/ProgramFiles/gromacs/bin directory: ./bdb2gmx_d Well, if this is what you typed, then I can see why it failed - typos will get you every time. If you did something else in the terminal and typed something else here, it's really impossible to know what's going on. Copy and paste from your terminal directly, and include any actual error messages. Proper sourcing of GMXRC should take care of this, as should appending to your PATH. Since neither worked, it's really hard to tell what's going on. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
Re: [gmx-users] SImulation with urea
Hi, I have some small doubt regarding using urea in simulation. Actually, I calculated the the number of urea molecules for a particular concentration in the box. For eg., the same box if filled with water occupies 43614 molecules of water and if I need to fill molecules of urea for 1M concentration, the values comes around 875. I added, those urea molecules using -ci and -nmol flags in genbox command. How to add the water now, i.e. the remaining 42379 water molecules. When I use genbox to add water it replaces those Urea molecules completely and add 43614 molecules. I even tried adding water and urea simultaneously, in that case the urea molecules are added as per the given number, but the number of water molecules added are lesser than 42379, which should be 43614. What am I going wrong ?? For adding water and urea simultaneously, I used the following command: genbox -cp newbox,gro -cs spc216.gro -ci Urea.gro -nmol 875 -o solv.gro -p topol.top Regards - Bharat -- 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] SImulation with urea
On 3/4/14, 6:10 PM, bharat gupta wrote: Hi, I have some small doubt regarding using urea in simulation. Actually, I calculated the the number of urea molecules for a particular concentration in the box. For eg., the same box if filled with water occupies 43614 molecules of water and if I need to fill molecules of urea for 1M concentration, the values comes around 875. I added, those urea molecules using -ci and -nmol flags in genbox command. How to add the water now, i.e. the remaining 42379 water molecules. When I use genbox to add water it replaces those Urea molecules completely and add 43614 molecules. I even tried adding water and urea simultaneously, in that case the urea molecules are added as per the given number, but the number of water molecules added are lesser than 42379, which should be 43614. What am I going wrong ?? For adding water and urea simultaneously, I used the following command: genbox -cp newbox,gro -cs spc216.gro -ci Urea.gro -nmol 875 -o solv.gro -p topol.top Doing these two processes simultaneously is asking for trouble and will probably fail. I don't understand the statement above about genbox removing urea - the program shouldn't do that (genion replaces molecules, genbox adds them). Do the additions in two steps: 1. Add urea with -ci -nmol 2. Simply fill the rest of the box like would would anything else with genbox -cs spc216.gro -cp system_with_urea_already_added.gro -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] gmx gangle in the development version of gromacs
Hello gromacs users, I want to analyze a liquid interface by producing a series of histograms that profile different slices of my simulation along the cartesian z axis. In each histogram, I want to bin the angles between the z-axis and the normal vector defined by a plane of three atoms in a flat molecular ring. I have many of these rings in my simulation. I downloaded the development version of gromacs and read the documentation associated with g_select and gmx gangle. As I understand it, my index file should select the atoms that define each normal vector. To properly profile a slice, the selection should be dynamic. Atoms *defining the plane* that drift into a slice during a simulation must be selected. Atoms *defining the plane* that drift out of a slice must be deselected. Also, it would be nice to make this spatial dynamic selection based on the center of geometry of the *atoms that define the plane* or some other sensible molecular substructure. My index file looks something like this... [ a_plane ] 1 2 3 10 11 12 ... ...where each row lists that ring atoms that define the plane in exactly the same way. Assuming I define a given slice to be between 0 and 1 on the z axis, I believe the command that will produce what I want is: gmx gangle -f file.trr -s file.tpr -n file.ndx -g1 plane -group1 'z 0 to 1 and group a_plane' -g2 z -oh file.xvg -binw 1.0 A few questions/comments: 1.) I am unsure how I should set the '-selrpos' option. The gangle program requires all three atoms to compute the angle so I suspect that the prefix 'whole_' is necessary. What is the difference between the res_ and mol_ infix? I was hoping the index file would restrict the computation of the reference position so that 'whole_res_cog' would work but it seems to compute the cog for the whole residue, not that atoms that define the plane. For clarity, if the cog of the three atoms that define the plane lie within the slice, I want all three atoms that define the plane to be selected. 2.) Is it possible to use a custom set of atoms for computation of the cog that differs from the atoms I want selected if this cog is within the slice? For example, consider benzene. The program gangle requires three benzene atoms to define a plane but the cog of these atoms is not the cog of the ring. I suspect this is not possible with the gromacs tools. 2.) It seems the flag '-oall' outputs the angles for all the normal vectors defined by the atoms in my index file. Is this want most users will want from this tool? If I have selection like 'z 0 to 1 and group a_plane', it makes more sense for '-oall' to print all the selected angles, correct? Best, Eric -- 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] pbc problems
Hello everyone! I am a new one of gromacs. When a simulation of protein in water is finished, should i first use the command of trjconv to remove pbc conditions(with nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some other parameters)? Is the result believable without removing the pbc conditions or it is necessary for some specific calculations? Most Gromacs programs deal with PBC with no manipulation required, some do not. g_rms needs a properly processed trajectory. -Justin Thank you for your response! As you said, i also found the Rmsd by using -nojump or -mol is different from that without these commands. And i can not decide which one is more accurate. Furthermore, can you list some other parameters that need removed pbc conditions? such as SDF calculation ... -- 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.
