[gmx-users] RE:RE: One question about Domain decomposition
Hi Thank you for your reply, Berk. I mean that every node has the topology of the whole system. Originally I thought every node has the positions and other properties(information in my last e-mail) of the atoms. I made a mistake obviously. But now, I don't know how do you store the information of the atoms. How do you orgnize the local home atoms and atoms which communicated from neighbour nodes? I think the charge groups' indices are not continuous in one local node, so I cann't understand the way you store the atoms' information. Can you explain to me in detail? Or give me a sketch map of your method? Thank you! Best wishes! xuji x...@home.ipe.ac.cn 2009-02-17 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files?
> Date: Tue, 17 Feb 2009 16:59:42 +1100 > From: dallas.war...@pharm.monash.edu.au > Subject: RE: [gmx-users] Possible to stop mdrun changing file names when > usingcheckpoint files? > To: gmx-users@gromacs.org > > Chris, > > > One option is to avoid checkpoint files all together. I personally use > > a grompp/mdrun cycle of ~2h segments that was historically done in > > order to utilize the -sort -shuffle options to gromacs 3. I found it > > simpler to keep on doing the exact same thing in gromacs 4, even > > though I no longer -sort or -shuffle. It appears to be working fine > > for me. I suspect that you could do the same type of thing via tpbconv. > > Yes, that is what I was doing previously and are continuing to do so with > some at the moment with 4.0.X I suppose the question is now, is it a more > continuous simulation to be using the checkpoint files, or does tpbconv with > the energy and trajectory files provide the same degree of accuracy? > The trajectory and energy file do not store all the state variables for all thermostats and barostats. But resetting these variables introduces such a small error in most cases that it is negligible. I think I'll add a -rename (or something like that) flag to mdrun, so you can control the renaming. Berk > Totally unrelated and a little nugget for people that happen to have an > iPhone or iPod touch, you can get an application called Molecules for free > that allows you to view .pdb files, download direct from the pdb database or > from custom location. > > Catch ya, > > Dr Dallas Warren > Pharmacy and Pharmaceutical Sciences > Monash University > > A polar bear is a Cartesian bear that has undergone a polar transformation _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files?
Chris, > One option is to avoid checkpoint files all together. I personally use > a grompp/mdrun cycle of ~2h segments that was historically done in > order to utilize the -sort -shuffle options to gromacs 3. I found it > simpler to keep on doing the exact same thing in gromacs 4, even > though I no longer -sort or -shuffle. It appears to be working fine > for me. I suspect that you could do the same type of thing via tpbconv. Yes, that is what I was doing previously and are continuing to do so with some at the moment with 4.0.X I suppose the question is now, is it a more continuous simulation to be using the checkpoint files, or does tpbconv with the energy and trajectory files provide the same degree of accuracy? Totally unrelated and a little nugget for people that happen to have an iPhone or iPod touch, you can get an application called Molecules for free that allows you to view .pdb files, download direct from the pdb database or from custom location. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Possible to stop mdrun changing file names when using checkpoint files?
One option is to avoid checkpoint files all together. I personally use a grompp/mdrun cycle of ~2h segments that was historically done in order to utilize the -sort -shuffle options to gromacs 3. I found it simpler to keep on doing the exact same thing in gromacs 4, even though I no longer -sort or -shuffle. It appears to be working fine for me. I suspect that you could do the same type of thing via tpbconv. Chris. -- original message -- Justin, When using checkpoint files to continue a run, mdrun overrides the output file names specified by putting ".part" before the file extension. I don't want it to do that, since I have already told it how I want the output files to be named. Is it possible to stop that happening? Try using -append. That adds it onto the previous files. Not what I want either. Way I have been doing my simulations is in batches of 1ns. Things drop out, stop, then get resubmitted to do another 1 ns. Before 4.0 have used tpb2conv -extend 1000 supplied with the energy and trajectory files. Minor thing I know, but when your various scripts are all set up to use a particular format, life is easier if you keep things are they are. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files?
Justin, >> When using checkpoint files to continue a run, mdrun overrides the output >> file names specified by putting ".part" before the file extension. >> >> I don't want it to do that, since I have already told it how I want the >> output files to be named. >> >> Is it possible to stop that happening? >Try using -append. That adds it onto the previous files. Not what I want either. Way I have been doing my simulations is in batches of 1ns. Things drop out, stop, then get resubmitted to do another 1 ns. Before 4.0 have used tpb2conv -extend 1000 supplied with the energy and trajectory files. Minor thing I know, but when your various scripts are all set up to use a particular format, life is easier if you keep things are they are. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Possible to stop mdrun changing file names when using checkpoint files?
Dallas B. Warren wrote: When using checkpoint files to continue a run, mdrun overrides the output file names specified by putting ".part" before the file extension. I don't want it to do that, since I have already told it how I want the output files to be named. Is it possible to stop that happening? Try using -append. -Justin Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Possible to stop mdrun changing file names when using checkpoint files?
When using checkpoint files to continue a run, mdrun overrides the output file names specified by putting ".part" before the file extension. I don't want it to do that, since I have already told it how I want the output files to be named. Is it possible to stop that happening? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] RE: Continuation of Runs and Checkpoint File Use
OK, well I got this wrong. If you want to extend or continue a simulation that has completed, you still have to use tpbconv. It is used to change the number of steps, then you feed that into mdrun with the checkpoint file. The only time you don't need tpbconv now is with a crashed simulation. I have added the information here: http://wiki.gromacs.org/index.php/Extending_Simulations Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Question about confining simulations to inert spherical pores
Hello, I'm interested in setting up a simulation in Gromacs based on a procedure from an interesting paper. The paper (available here: http://tinyurl.com/cp4qbu) describes simulating peptides confined to inert spherical pores. I'm not yet an advanced Gromacs user, and so I was hoping someone in the Gromacs community would be able to mention the steps necessary to build an inert spherical pore for simulation with Gromacs. Any help is greatly appreciated! Best regards, Chester ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] The difference about NPT and NVT ensemble.
> I have some questions about ensemble. Would you please tell me about NPT or > NVT ensemble? What difference about them? http://wiki.gromacs.org/index.php/Molecular_Dynamics_Simulations Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] The difference about NPT and NVT ensemble.
fufengliu wrote: Hello, everyone, I have some questions about ensemble. Would you please tell me about NPT or NVT ensemble? What difference about them? And how to define in the molecular dynamics mdp file? What ensemble does the below parameters extracted from my mdp file? NPT = constant Number of molecules, Pressure, Temperature NVT = constant Number of molecules, Volume, Temperature If you are blindly writing .mdp parameters without knowing what you are doing, you had better re-think your approach. Your comments in the file will tell you what you are doing. Sounds like some textbook reading (regarding ensembles) would be useful, as well as a thorough read of the Gromacs manual to learn what the options are doing. -Justin ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Thank you for your kind consideration of these questions. Sincerely, Fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] The difference about NPT and NVT ensemble.
Hello, everyone, I have some questions about ensemble. Would you please tell me about NPT or NVT ensemble? What difference about them? And how to define in the molecular dynamics mdp file? What ensemble does the below parameters extracted from my mdp file? ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Thank you for your kind consideration of these questions. Sincerely, Fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to show the created box?
package require pbctools pbc box should do it. On Sun, Feb 15, 2009 at 10:29 PM, Chih-Ying Lin wrote: > HI > after creating the box, and write it into .gro file. > > when i try the .gro file with VMD, but the box is not shown. > > how can i show the created box with VMD? > > thank you > > > Lin > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to show the created box?
If your box is very big, VMD may run out all your computer's memory and crash. You can copy your GRO file and erase some water molecules in the middle of the GRO file copy, for you see the extremes of your water box. Kind regards. -- From: "Mark Abraham" Sent: Sunday, February 15, 2009 10:33 PM To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] How to show the created box? Chih-Ying Lin wrote: HI after creating the box, and write it into .gro file. when i try the .gro file with VMD, but the box is not shown. how can i show the created box with VMD? You should start by looking in the VMD help and/or manual :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Oscillating Electrical Field
Hi I'm trying to create an oscillating electrical field in my simulation, and I was hoping that someone who had successfully done this in the past could please offer some advice on the choice of parameters in my mdp. Eventually, I would like to create a system with oscillating fields across both x and y, pi/2 radians out of phase in order to cause a body in my simulation to rotate by aligning its charge distribution to the field. At the moment, I would just like to find out a couple of things about exactly which parameters to use. I've looked at the source code from src/mdlib/sim_util.c and tried out a few combinations, and as far as I can see you need to enter parameters for the x axis (as an example) in both E_x and E_xt, representing the maximum field strength. E_x values are chosen as described in the manual. E_xt takes three values- the first value has to be 1 (to generate an oscillating field), the second value a number related to the frequency of the wave, and the third value a measure of phase so that you can vary the starting values of the field. Other values are ignored. My first question is have I interpreted these values correctly? Also, the code refers to t, which I assume to be the time. What is the units of t, and does to cosine function expect radians or degrees? Also, there seems to be an optional term which causes the waves to decrease exponentially over time- Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2]))); can I turn this off or ignore it if I want to specify a phase? Many thanks in advance Ben Benjamin A. Hall Structural Bioinformatics & Computational Biochemistry Unit / OCISB University of Oxford http://sbcb.bioch.ox.ac.uk/hall.php +44 (0)1865 613304 benjamin.h...@bioch.ox.ac.uk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] One question about Domain decomposition
Hi, Your question is too vague for me to answer. What do you mean with "all the molecules"? And what do you mean with information? Every node knows the topology of the whole system. But each node only knows the coordinates and velocities of its local atoms plus the coordinates of some atoms of neighboring nodes. Berk > Date: Mon, 16 Feb 2009 22:45:43 +0800 > From: x...@home.ipe.ac.cn > To: gmx-users@gromacs.org > Subject: [gmx-users] One question about Domain decomposition > > > Hi all Gromacs users: > > These days I read the codes about domain decomposition of Gromcas-4.0. > It seems that every node which is used to deal with one real space > domain has all of the molecules' information as in the particle > decomposition. > Is my comprehension right? And if it's wrong how is the molecules' > information stored in domain decomposition of Gromacs-4.0 ? > > Appreciate any help in advance! > > Best > wishes! > > > xuji > x...@home.ipe.ac.cn > 2009-02-16 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] One question about Domain decomposition
Hi all Gromacs users: These days I read the codes about domain decomposition of Gromcas-4.0. It seems that every node which is used to deal with one real space domain has all of the molecules' information as in the particle decomposition. Is my comprehension right? And if it's wrong how is the molecules' information stored in domain decomposition of Gromacs-4.0 ? Appreciate any help in advance! Best wishes! xuji x...@home.ipe.ac.cn 2009-02-16 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] .mdp file for polymer
Hi,
You should be much more precise in describing your problems.
gmxdump does not seem to give a segv at all.
Also you did not mail me your Gromacs version.
mdrun immediately gives a warning:
Warning: 1-4 interaction between 1 and 28 at distance 0.982 which is larger
than the 1-4 table size 0.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
You seem to have reduced the table size from the default 1.0 to 0.5.
But if interactions are beyond the table size, you need to increase the table.
Also your cut-off's are 0.1 nm, which is much smaller than the size of your
atoms.
This simulation setup is complete nonsens.
You can never expect a system to run propely with these kind of settings.
Berk
Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautha...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] .mdp file for polymer
Hello sir,
On giving gmxdump its giving me an error saying "segmentation fault.My box size
is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with
columb type=PME. I read from mailing list that PME calculations requires large
amount of memory space.Is this an issue with dimension of box or with the
system memory allocation ?Here's my log file.
T-Coupling : 106 (total 106 atoms)
Energy Mon. : 106 (total 106 atoms)
Acceleration: 106 (total 106 atoms)
Freeze : 106 (total 106 atoms)
User1 : 106 (total 106 atoms)
User2 : 106 (total 106 atoms)
VCM : 106 (total 106 atoms)
XTC : 106 (total 106 atoms)
Or. Res. Fit: 106 (total 106 atoms)
QMMM: 106 (total 106 atoms)
ben-nch0.xtc frame 0:
natoms= 1 step= 0 time=-2.9120485e-05 prec=2.8026e-45
box (3x3):
box[0]={-2.89059e-05, 3.98821e-34, -2.39380e-05}
box[1]={ 3.98770e-34, 1.40130e-45, -2.91168e-05}
box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
x (1x3):
Segmentation fault
_
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Re: [gmx-users] Problem using MPIRUN MDRUN
fpri...@nimr.mrc.ac.uk wrote: I did not stop the simulation manually and it did not give a segmentation fault message, but something else that I have never seen before (and actually, I am still not understanding the error message). Now I'm running the dynamics on my machine, instead of running it on the cluster, and there are no problems at all. This means that the problem is not related to my protein or to the parameters of the dynamic, but it must be somewhere else in the mpirun command line or something like that. OK, so there's probably some problem with file system availability on the cluster, and/or returning output files to the user. We can't help you there. This sort of detail and differential diagnosis would have been a good thing to say the first time you described your problem. See the final link here - http://wiki.gromacs.org/index.php/Support grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_s -s file.tpr -o file.trr -c file.gro -np 32 This looks like asking for trouble, if _s and _d are your suffixes for single and double. Don't mix them. If you've erroneously retyped them, then that's not helpful information for us. Computers are literal, and we can only help you work out what you've told it wrongly if you tell us the same thing - so write a script and/or copy-paste things so that you are reproducible. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] extrnal itp files
What do you mean by directions? in your topology file you have to include the file martini_v2.1.itp as you would do for any other force field! On Feb 16, 2009, at 11:07 AM, bhf70 wrote: It is possible to set an example ? bhf70 wrote: > Could you tell me, please. > > What's directions need the programm pdb2gmx to use external .itp files, > for example martini_v2.1.itp (Coarse Grained Force Field)? > > How is it to do ? There should be instructions accompanying that force field wherever you got it from. There's some general information here http://wiki.gromacs.org/index.php/Include_File_Mechanism Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Re: [gmx-users] extrnal itp files
It is possible to set an example ? bhf70 wrote: > Could you tell me, please. > > What's directions need the programm pdb2gmx to use external .itp files, > for example martini_v2.1.itp (Coarse Grained Force Field)? > > How is it to do ? There should be instructions accompanying that force field wherever you got it from. There's some general information here http://wiki.gromacs.org/index.php/Include_File_Mechanism Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to show the created box?
There is a script in vmd to do it. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 16/02/2009, at 3:30 PM, "Chih-Ying Lin" wrote: HI after creating the box, and write it into .gro file. when i try the .gro file with VMD, but the box is not shown. how can i show the created box with VMD? thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Problem using MPIRUN MDRUN
I did not stop the simulation manually and it did not give a segmentation fault message, but something else that I have never seen before (and actually, I am still not understanding the error message). Now I'm running the dynamics on my machine, instead of running it on the cluster, and there are no problems at all. This means that the problem is not related to my protein or to the parameters of the dynamic, but it must be somewhere else in the mpirun command line or something like that. grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_s -s file.tpr -o file.trr -c file.gro -np 32 - Original Message - From: Mark Abraham Date: Friday, February 13, 2009 10:11 pm Subject: Re: [gmx-users] Problem using MPIRUN MDRUN > fpri...@nimr.mrc.ac.uk wrote: > > Thanks a lot, I'll check stderr and stdout, because I think that > the log file is correct (it looks like a normal dynamic that has > been manually interrupted). > > If you've manually interrupted the simulation, then you cannot > expect > the buffered I/O to be correctly formed. > > > The system is not exploded cause it does not generate the gro > file and step files. > > If there's no final coordinate file (.gro by default), then the > simulation did not complete correctly. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] .mdp file for polymer
Hi,
Independent of any other problems you might have, gmxdump should never give a
segmentation fault.
Could you mail me the tpr file?
Which version of Gromacs are you using?
Berk
Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautha...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] .mdp file for polymer
Hello sir,
On giving gmxdump its giving me an error saying "segmentation fault.My box size
is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with
columb type=PME. I read from mailing list that PME calculations requires large
amount of memory space.Is this an issue with dimension of box or with the
system memory allocation ?Here's my log file.
T-Coupling : 106 (total 106 atoms)
Energy Mon. : 106 (total 106 atoms)
Acceleration: 106 (total 106 atoms)
Freeze : 106 (total 106 atoms)
User1 : 106 (total 106 atoms)
User2 : 106 (total 106 atoms)
VCM : 106 (total 106 atoms)
XTC : 106 (total 106 atoms)
Or. Res. Fit: 106 (total 106 atoms)
QMMM: 106 (total 106 atoms)
ben-nch0.xtc frame 0:
natoms= 1 step= 0 time=-2.9120485e-05 prec=2.8026e-45
box (3x3):
box[0]={-2.89059e-05, 3.98821e-34, -2.39380e-05}
box[1]={ 3.98770e-34, 1.40130e-45, -2.91168e-05}
box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
x (1x3):
Segmentation fault
_
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Re: [gmx-users] extrnal itp files
bhf70 wrote: Could you tell me, please. What's directions need the programm pdb2gmx to use external .itp files, for example martini_v2.1.itp (Coarse Grained Force Field)? How is it to do ? There should be instructions accompanying that force field wherever you got it from. There's some general information here http://wiki.gromacs.org/index.php/Include_File_Mechanism Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] .mdp file for polymer
varsha gautham wrote:
Hello sir,
On giving gmxdump its giving me an error saying "segmentation fault.
99.9% of the time there is more information available. Check your
stdout, stderr and the .log file.
My
box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5
timesteps and with columb type=PME. I read from mailing list that PME
calculations requires large amount of memory space.Is this an issue with
dimension of box or with the system memory allocation ?Here's my log file.
You don't need/want PME for a system with only 106 atoms. A vacuum
simulation also isn't likely to tell you anything useful.
T-Coupling : 106 (total 106 atoms)
Energy Mon. : 106 (total 106 atoms)
Acceleration: 106 (total 106 atoms)
Freeze : 106 (total 106 atoms)
User1 : 106 (total 106 atoms)
User2 : 106 (total 106 atoms)
VCM : 106 (total 106 atoms)
XTC : 106 (total 106 atoms)
Or. Res. Fit: 106 (total 106 atoms)
QMMM: 106 (total 106 atoms)
ben-nch0.xtc frame 0:
natoms= 1 step= 0 time=-2.9120485e-05 prec=2.8026e-45
box (3x3):
box[0]={-2.89059e-05, 3.98821e-34, -2.39380e-05}
box[1]={ 3.98770e-34, 1.40130e-45, -2.91168e-05}
box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
x (1x3):
Segmentation fault
___
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[gmx-users] extrnal itp files
Could you tell me, please. What's directions need the programm pdb2gmx to use external .itp files, for example martini_v2.1.itp (Coarse Grained Force Field)? How is it to do ? I use GROMACS v3.3.2 and OPLSAA Force Field. Igor ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] .mdp file for polymer
Hello sir,
On giving gmxdump its giving me an error saying "segmentation fault.My box
size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps
and with columb type=PME. I read from mailing list that PME calculations
requires large amount of memory space.Is this an issue with dimension of box
or with the system memory allocation ?Here's my log file.
T-Coupling : 106 (total 106 atoms)
Energy Mon. : 106 (total 106 atoms)
Acceleration: 106 (total 106 atoms)
Freeze : 106 (total 106 atoms)
User1 : 106 (total 106 atoms)
User2 : 106 (total 106 atoms)
VCM : 106 (total 106 atoms)
XTC : 106 (total 106 atoms)
Or. Res. Fit: 106 (total 106 atoms)
QMMM: 106 (total 106 atoms)
ben-nch0.xtc frame 0:
natoms= 1 step= 0 time=-2.9120485e-05 prec=2.8026e-45
box (3x3):
box[0]={-2.89059e-05, 3.98821e-34, -2.39380e-05}
box[1]={ 3.98770e-34, 1.40130e-45, -2.91168e-05}
box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
x (1x3):
Segmentation fault
___
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