RE: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun
I have checked my job on another cluster which is dual core. On one node, it
just ran fine! I think sth might be wrong with the cluster settings. I will
try the output settings you suggested as well. I will keep you posted.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Friday, September 04, 2009 5:29 PM
To: Gromacs Users' List
Subject: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun
Have you tried my suggestion from the last message of setting frequent
output?
Could your system just be collapsing at the outset of the simulation?
Setting
nstxout = 1 would catch something like this.
There is nothing special about treating a protein in parallel vs. a system
of
water. Since a system of water runs just fine, it seems even more likely to
me
that your system is simply crashing immediately, rather than a problem with
Gromacs or the MPI implementation.
-Justin
Paymon Pirzadeh wrote:
> Regarding the problems I have on running protein system in parallel
> (runs without output), When I run pure water system, everything is fine,
> I have tested pure water systems 8 times larger than my protein system.
> while the former runs fine, the latter has problems. I have also tested
> pure water systems with approximately same number of sites in .gro file
> as in my protein .gro file, and with the same input file in terms of
> spitting outputs; they are fine.I would like to know what happens to
> GROMACS when a protein is added to the system. The cluster admin has not
> get back to me, but I still want to check there is no problem with my
> setup! (although my system runs fine in serial mode).
> Regards,
>
> Payman
>
>
>
> On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote:
>> Payman Pirzadeh wrote:
>>> There is sth strange about this problem which I suspect it might be due
to
>>> the mdp file and input. I can run the energy minimization without any
>>> problems (I submit the job and it apparently works using the same
submission
>>> script)! But as soon as I prepare the tpr file for MD run, then I run
into
>>> this run-without-output trouble.
>>> Again I paste my mdp file below (I want to run an NVT run):
>>>
>> There isn't anything in the .mdp file that suggests you wouldn't get any
output.
>> The output of mdrun is buffered, so depending on your settings, you may
have
>> more frequent output during energy minimization. There may be some
problem with
>> the MPI implementation in buffering and communicating data properly.
That's a
>> bit of a guess, but it could be happening.
>>
>> Definitely check with the cluster admin to see if there are any error
messages
>> reported for the jobs you submitted.
>>
>> Another test you could do to force a huge amount of data would be to set
all of
>> your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter
simulation (to
>> prevent massive data output!); this would force more continuous data
through the
>> buffer.
>>
>> -Justin
>>
>>> cpp = cpp
>>> include = -I../top
>>> define = -DPOSRES
>>>
>>> ; Run control
>>>
>>> integrator = md
>>> dt = 0.001 ;1 fs
>>> nsteps = 300 ;3 ns
>>> comm_mode= linear
>>> nstcomm = 1
>>>
>>> ;Output control
>>>
>>> nstxout = 5000
>>> nstlog = 5000
>>> nstenergy= 5000
>>> nstxtcout= 1500
>>> nstvout = 5000
>>> nstfout = 5000
>>> xtc_grps =
>>> energygrps =
>>>
>>> ; Neighbour Searching
>>>
>>> nstlist = 10
>>> ns_type = grid
>>> rlist= 0.9
>>> pbc = xyz
>>>
>>> ; Electrostatistics
>>>
>>> coulombtype = PME
>>> rcoulomb = 0.9
>>> ;epsilon_r= 1
>>>
>>> ; Vdw
>>>
>>> vdwtype = cut-off
>>> rvdw = 1.2
>>> DispCorr = EnerPres
>>>
>>> ;Ewald
>>>
>>> fourierspacing = 0.12
>>> pme_order = 4
>>> ewald_rtol = 1e-6
>>> optimize_fft= yes
>>>
>>> ; Temperature coupling
>>>
>>> tcoupl = v-rescale
>>> ld_seed = -1
>>> tc-grps = System
>>> tau_t= 0.1
>>> ref_t= 275
>>>
>>> ; Pressure Coupling
>>>
>>> Pcoupl = no
>>> ;Pcoupltype = isotropic
>>> ;tau_p= 1.0
>>> ;compressibility = 5.5e-5
>>> ;ref_p= 1.0
>>> gen_vel = yes
>>> gen_temp = 275
>>> gen_seed = 173529
>>> constraint-algorithm = Lincs
>>> constraints = all-bonds
>>> lincs-order = 4
>>>
>>> Regards,
>>>
>>> Payman
>>>
>>>
>>> -Original Message-
>>> From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
>>> On Behalf Of Mark Abraham
>>> Sent: August 27, 2009 3:32 PM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] Re: wierd behavior of mdrun
>>>
>>> Vitaly V. Chaban wrote:
Then I believe you have problems with MPI.
>
[gmx-users] Re: DMF topology file
Hi Abhishek, I know two possible ways. The first is to find PBD file of DMF (one molecule) and then use x2top program of the gromacs package. When asked for a FF, OPLS/AA can be pointed out. DMF contains only common atoms, so I guess there will be no problems to generate the topology automatically. The second way is to make topology by hand. If one has enough experience it can be of some pleasure. :) Good luck! Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, cell.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === On Sat, Sep 5, 2009 at 3:20 PM, Abhishek Banerjee wrote: > hi Vitaly, > Thanks for your help. I have created a DMF box. Now I want > to do NTP and NVT on that. For that I want to use OPLS/AA force field. I got > some reference paper on that. How can I go to create a itp or top for DMF. > If you give me some hints about the steps to crate a topology file for > DMF(OPLS/AA), will be greate help for me. > thanks > abhishek > > -- > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] PMF and pull with membrane helix
On Sep 5, 2009, at 7:42 AM, Ragnarok sdf wrote: Hi I am trying to calculate the PMF by pulling two membrane protein monomers apart using the pull code with umbrella sampling. While trying to generate my reaction path, no matter how slow I pull, my helix starts bending (not really bending, but it kind of tends to transform into a "C" shape inside my bilayer). Since I am only simulating a small part of what would a be a very big transmembrane receptor, I thought about restraining the movement along the z axis of my terminal residues, sort of simulating the "weight" that would exist if the entire intracellular and extracellular domains were there. My protocol to obtain the PMF is to use this first pulling protocol only to generate the different windows (distance between the two monomers) in each of which I would use the umbrella sampling (maintaining the force constant and switching off the pull_rate) to generate data to perform WHAM analysis. So that leaves me with two questions. First is: would I, by restraining the movement along the Z axis, create artifacts that would be computed and ruin my PMF calculation? Technically speaking, no. But you should correct for the energy of imposing the alignment with the z axis. And second: Would this be a correct PMF protocol? That would just give you the PMF of the two transmembrane segments given their fixed relative orientations, which might be questionable in regard to its relevance but may be not! It is however strange that you have this C shape even with the slow pulling. You might want to check your parameters/procedure. You might need a long period of "relaxation/equilibration" to remove the C shape, which suggests that you are still pulling too fast! XAvier. Thank you in advance FabrÃcio Bracht ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] grompp error in peptide-membrane simulations
afsaneh maleki wrote: Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: >Fetal error : Atomtype LC3 not found! (this is atomtype of the lipide) This is my complex.top file #include "protein.itp" #include "dopc.itp" #include "lipid.itp" #include "tip3p.itp" #include "ions.itp" [system] ;name protein on sur+relaxed dopc [molecules] ;namenumber Protein 1 DOPC 128 SOL 4086 SOD 6 CLA 8 --- this atomtype (LC3) is in the dopc.itp and lipid.itp files but don't find in ffG43a2.rtp and .atp. i'm sure structure file is n't different in terms of the number of atoms , atomnames and the order of them with .itp files. any help will be hightly appreciated. Your topology file is set up incorrectly. Might I suggest the tutorial I wrote for membrane protein simulations: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html There is also helpful information on the wiki site (http://oldwiki.gromacs.org) about running membrane simulations and doing analysis. -Justin -- Afsaneh Maleki PhD student of physical chemistry Department of chemistry, Isfahan Univ. of Tech. Isfahan 84156-83111, Iran ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate ICTAS Doctoral Scholar 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/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] grompp error in peptide-membrane simulations
Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: >Fetal error : Atomtype LC3 not found! (this is atomtype of the lipide) This is my complex.top file #include "protein.itp" #include "dopc.itp" #include "lipid.itp" #include "tip3p.itp" #include "ions.itp" [system] ;name protein on sur+relaxed dopc [molecules] ;namenumber Protein 1 DOPC 128 SOL 4086 SOD 6 CLA 8 --- this atomtype (LC3) is in the dopc.itp and lipid.itp files but don't find in ffG43a2.rtp and .atp. i'm sure structure file is n't different in terms of the number of atoms , atomnames and the order of them with .itp files. any help will be hightly appreciated. -- Afsaneh Maleki PhD student of physical chemistry Department of chemistry, Isfahan Univ. of Tech. Isfahan 84156-83111, Iran ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Re: wierd behavior of mdrun
Have you tried my suggestion from the last message of setting frequent output? Could your system just be collapsing at the outset of the simulation? Setting nstxout = 1 would catch something like this. There is nothing special about treating a protein in parallel vs. a system of water. Since a system of water runs just fine, it seems even more likely to me that your system is simply crashing immediately, rather than a problem with Gromacs or the MPI implementation. -Justin Paymon Pirzadeh wrote: Regarding the problems I have on running protein system in parallel (runs without output), When I run pure water system, everything is fine, I have tested pure water systems 8 times larger than my protein system. while the former runs fine, the latter has problems. I have also tested pure water systems with approximately same number of sites in .gro file as in my protein .gro file, and with the same input file in terms of spitting outputs; they are fine.I would like to know what happens to GROMACS when a protein is added to the system. The cluster admin has not get back to me, but I still want to check there is no problem with my setup! (although my system runs fine in serial mode). Regards, Payman On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote: Payman Pirzadeh wrote: There is sth strange about this problem which I suspect it might be due to the mdp file and input. I can run the energy minimization without any problems (I submit the job and it apparently works using the same submission script)! But as soon as I prepare the tpr file for MD run, then I run into this run-without-output trouble. Again I paste my mdp file below (I want to run an NVT run): There isn't anything in the .mdp file that suggests you wouldn't get any output. The output of mdrun is buffered, so depending on your settings, you may have more frequent output during energy minimization. There may be some problem with the MPI implementation in buffering and communicating data properly. That's a bit of a guess, but it could be happening. Definitely check with the cluster admin to see if there are any error messages reported for the jobs you submitted. Another test you could do to force a huge amount of data would be to set all of your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter simulation (to prevent massive data output!); this would force more continuous data through the buffer. -Justin cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: August 27, 2009 3:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: wierd behavior of mdrun Vitaly V. Chaban wrote: Then I believe you have problems with MPI. Before I experienced something alike on our old system - serial version worked OK but parallel one failed. The same issue was with CPMD by the way. Another programs worked fine. I didn't correct that problem... On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh wrote: Yes, it works when it is run on one processor interactively! That's fine, but it doesn't mean the problem is with the parallelism, as Vitaly suggests. If your cluster filesystem isn't configured properly, you will observe these symptoms. Since the submission script was the same, MPI worked previously, so isn't likely to be the problem... Mark On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an emp
