Re: [gmx-users] Cosine content
Hey :) This is pretty incorrect... A high cosine content is an indicator of unidirectional motion in phase space. I've elaborated on that on this list some while ago. Regarding your case, this means that, even if the RMSD is stable starting from 5ns, the protein still experiences random motions. So the opposite is true: the protein configuration is adrift, i.e., it's undergoing conformational rearrangement, not random (thermal) fluctuations. This rearrangement may happen in phase space far away from the reference structure, thus not noticeable in the RMSD, which will just say 'far away' (the larger the RMSD, the larger the volume of phase space to be moving in). You should therefore consider as statistically relevant the trajectory starting from 30ns. Arguable. The conformational rearrangement may be relevant and it may even be a functional mode, which is just undersampled. Basing on my experience, I advice you to extend the simulation lenght (i.e.100ns) to ensure a larger dataset. Of course, sampling longer makes sense :) Il 14/12/2011 00:37, R.S.K.Vijayan ha scritto: I have a 50 ns trajectory and looking at the RMSD plot, i set aside the first 5 ns as the time required for stabilization and subsequently carried out a essential dynamics for the backbone atoms post 5ns. It is very likely that equilibration of the system takes longer than 5ns. Actually it is highly unlikely that it has converged with 5ns. But when i perform a cosine content analysis for the eigen vector 1, i get these strange results a) Performing a g_analyze run using -b 5000 to -e 5 ( ie 5- 50 ns ) produces a cosine value of 0.92 This suggests a transition. Look a the RMSD matrix for the trajectory to see if you can spot a transition. As mentioned above, the transition may be part of the equilibration, or reflect a functional mode. That should be assessed using extended simulation(s). but when i perform a cosine analysis using -b 5000 to -e 25000 ( 5-25ns) i get a cosine value of 0.24 also when i perform a cosine analysis using -b 3 to -- 5(30-50 ns) i get a cosine value of 0.05 so how should i interpret this result, It's like doing PCA on the position of a canoe around a waterfall. If you look at the whole stretch, including the drop down, you'll see the thing getting closer to the fall more and more rapidly, taking the plunge and then being pushed away from the fall. If you only look at what happens before, there's just a slow drift towards the waterfall. If you only look at the what happens after, the canoe is just wobbling in the pond below randomly. does it imply that all the conformational changes are taking place between 30 to 50 ns No, there appears to be a conformational rearrangement before 30ns. Likely most obvious between 20 and 30 ns. Again, look at the RMSD matrix. or is there some thing wrong with the convergence of the system??? Papers tell that the cosine value does decreases with increased time scale due to enhanced sampling, but strange a 25 ns simulation has a low cosine value on the contrary a 50 ns simulation has an increased cosine value. Nothing strange. It depends on the system and what is happening in it. But it doesn't exclude the possibility of bad convergence. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Coupling groups for nvt equilibration
Thanks Justin. I have tried both ways now and considering Protein_MG_GDP and Water_ions groups, it is running without any error but Protein_GDP and MG_Water_ions is failing with an error message. Thanks again... Neeru neeru sharma wrote: Thanks Justin. I tried the simulation with Protein_GDP and Water_ions, considering that Water_and_ions group will include MG. But it didn't work showing an error,saying One atom not present in the coupling group. Shall I try to include MG in Water_ions group via make_ndx ? I think the better approach is the one you posted before. -Justin Neeru neeru sharma wrote: Dear Gromacs users, I am simulating a system containing a protein with covalently attached Mg in complex with GDP. For nvt equilibration, I have taken protein+Mg+GDP as the single group and Water+ions as the other. The corresponding block from the .mdp file is below: -- ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein_MG_GDP Water_and_ions Is this coupling method correct, to treat Protein and Mg as different quantities? You are not treating them differently; they are in a merged group. Note, though, that the default Water_and_ions group will include MG, and thus grompp with throw a fatal error. You'll have to create a custom group for this one, as well. Otherwise, the approach seems reasonable to me. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] submission error
Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Please anyone can help with this error. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] submission error
On 14/12/2011 10:30 PM, aiswarya pawar wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Looks like a problem with file writing privileges or maybe disk quota. Either make a new run directory or clean up before using this job script, and see how you go. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear gromacs users, I used g_covar in order to get the eigenvectors of a MD simulation. Analysis of the eigenvalue plot showed the high eigenvalue of the first eigenvector. I also used gmxdump in order to analyse eigenvec.trr. Frame 1 of the eigenvec.trr shows the eigenvector direction of each atom of eigenvector 1. I was wondering if there is a single XYZ-Direction (only one general direction, not for each atom) of this first eigenvector because to my (basic) knowledge, there should be an eigenvector direction corresponding to the eigenvalue in the eigenvalue plot. Thank you in advance Tobias PhD Student University of Vienna Austria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] XYZ-Direction of eigenvector
Dear gromacs users, I used g_covar in order to get the eigenvectors of a MD simulation. Analysis of the eigenvalue plot showed the high eigenvalue of the first eigenvector. I also used gmxdump in order to analyse eigenvec.trr. Frame 1 of the eigenvec.trr shows the eigenvector direction of each atom of eigenvector 1. I was wondering if there is a single XYZ-Direction (only one general direction, not for each atom) of this first eigenvector because to my (basic) knowledge, there should be an eigenvector direction corresponding to the eigenvalue in the eigenvalue plot. Thank you in advance Tobias PhD Student University of Vienna Austria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] XYZ-Direction of eigenvector
On 14/12/2011 11:20 PM, Linder Tobias wrote: Dear gromacs users, I used g_covar in order to get the eigenvectors of a MD simulation. Analysis of the eigenvalue plot showed the high eigenvalue of the first eigenvector. I also used gmxdump in order to analyse eigenvec.trr. Frame 1 of the eigenvec.trr shows the eigenvector direction of each atom of eigenvector 1. I was wondering if there is a single XYZ-Direction (only one general direction, not for each atom) of this first eigenvector because to my (basic) knowledge, there should be an eigenvector direction corresponding to the eigenvalue in the eigenvalue plot. You removed the global motion when you fitted to a reference structure, so all the remaining motion is internal. So you need to expect that the set of orthonormal vectors, in whose directions the mean-squared fluctuations are independent of each other (i.e. the eigenvectors of the eigenvalues you found), will generally have contributions from every remaining degree of freedom. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Coupling groups for nvt equilibration
neeru sharma wrote: Thanks Justin. I have tried both ways now and considering Protein_MG_GDP and Water_ions groups, it is running without any error but Protein_GDP and MG_Water_ions is failing with an error message. Well, without knowing the exact error message and all the steps you did preceding that to set up the index groups, there's nothing anyone can do to help, though I don't think it's necessary anyway. You have a set of groups that's working and that makes sense for your system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] submission error
Mark, I still the same error. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 14 Dec 2011 23:03:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] submission error On 14/12/2011 10:30 PM, aiswarya pawar wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Looks like a problem with file writing privileges or maybe disk quota. Either make a new run directory or clean up before using this job script, and see how you go. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] submission error
aiswarya.pa...@gmail.com wrote: Mark, I still the same error. Check the .log file for any errors, and if you find none, then the problem isn't from Gromacs and should be investigated with your sysadmin. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 14 Dec 2011 23:03:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] submission error On 14/12/2011 10:30 PM, aiswarya pawar wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Looks like a problem with file writing privileges or maybe disk quota. Either make a new run directory or clean up before using this job script, and see how you go. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Help with g_rmsf
Hi everyone, please I have a litle problem: during my simulation, the dimer I'm simulating changed a lot. So when I calculate with g_rms, the RMSD between my initial and my final structure (choosing Protein-H), I get a value of 10 angstroms. However, when I try to calculate a RMSDeviation averaged over residue using g_rmsf -od , between the first chain of the initial and final structure, I get RMSDeviation per residue values that don't exceed 3 or 4 angstroms. Please can anyone explain how g_rmsf works? If I do the following: g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose chainA-H), does g_rmsf fit one the whole dimer and then calculate rmsdeviation of chainA or does it fit on chainA and then calculate RMSdeviation of chainA. In the latter case, my result does not reflect the reality of my simulation. Please if anyone knows the answer, I would really appreciate some help. Thanks, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topology and parameter for cobalt metal
Dear all I am interested in simulating a model protein with cobalt forming coordinate bond with His. I coud'nt find entry for cobalt in any forcefield .rtp file. I am using Gromacs 4.5.4 . If any one can help me in getting forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with g_rmsf
Hi Carla, during my simulation, the dimer I'm simulating changed a lot. So when I calculate with g_rms, the RMSD between my initial and my final structure (choosing Protein-H), I get a value of 10 angstroms. Have you made sure there are no atoms jumping across the boundaries? g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose chainA-H), If you choose chainA-H, you'll get results for that chain. It will be used for the fit as well as for the analysis. does g_rmsf fit one the whole dimer and then calculate rmsdeviation of chainA or does it fit on chainA and then calculate RMSdeviation of chainA. In the latter case, my result does not reflect the reality of my simulation. It does reflect the reality of your simulation. Maybe it does not reflect what you aimed to get. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology and parameter for cobalt metal
shahid nayeem wrote: Dear all I am interested in simulating a model protein with cobalt forming coordinate bond with His. I coud'nt find entry for cobalt in any forcefield .rtp file. I am using Gromacs 4.5.4 . If any one can help me in getting forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Standard, non-polarizable MM force fields are not particularly well-suited for dealing with transition metals. Fixed point charges on such species, especially those coordinated to amino acids, are generally very incorrect, not to mention geometric coordination parameters that are not built-in. http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] nrexcl = 2 or 3?
Dear GMXers, I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3? According to the manual (v 4.5), nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away. In charmm ff, 1-4 interactions are needed and it is no further than 3 bonds away, so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have charges. If I use nrexcl =3, no electrostatics energy is reported while the value matches with the one calculated by hand when I set nrexcl to be 2. Your clarification is greatly appreciated. Luke -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to use g_dipoles
dear users: I am using Gromacs 4.0.5. My system consist of chared plain and charged protein. How can i use the g_dipoles to get the protein's dipole? what is the exact option? Thanks! Lee -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] submission error
Am using mipch2-1.2.7. Is this the problem? Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: aiswarya.pa...@gmail.com Date: Wed, 14 Dec 2011 13:09:19 To: Gromacs mailgmx-users@gromacs.org Reply-To: aiswarya.pa...@gmail.com Subject: Re: [gmx-users] submission error Mark, I still the same error. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 14 Dec 2011 23:03:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] submission error On 14/12/2011 10:30 PM, aiswarya pawar wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Looks like a problem with file writing privileges or maybe disk quota. Either make a new run directory or clean up before using this job script, and see how you go. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Protein-MG-GDP (Protein-Ion-ligand) system simulation
Dear Gromacs users, I have to simulate a system consisting of Protein+MG+GDP where Protein is in complex with MG and GDP. I generated the GDP parameters using antechamber and then converted the topology,coordinate and parameter files to the corresponding gromacs format. Then, I tried to start with the simulation using AMBER ff03 forcefield. The system ran well till energy minimization step, but at equilibration steps it is showing lincs error at NVT equilibration step. I used 2 coupling groups for my system with lincs constraint algorithm as follows: *tc-grps = Protein_MG_GDP Water_and_ions * I tried turning off lincs warning too, den NVT equilibration was done finely but the system was blowing up during NPT equilibration. I tried with 3-4 steps of minimization also, but it didnt work (I have tried with lincs warning off in NPT too). I have visualized the NVT output trajectory and compared it with the initial structure too, and the trajectory was fine. I am unable to figure out the reason for why the system is blowing up. I am following the drug-ligand simulation tutorial but still can't figure out the problem. Can anyone suggest any possible means to overcome this situation? If anyone has simulated any similar system with Protein-ion-ligand complex or have faced similar problem, please share with what to do now to resolve this issue or to simulation such a system? Any help will be highly appreciated. Thanks - Neeru Sharma, Pune (India) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Protein-MG-GDP (Protein-Ion-ligand) system simulation
neeru sharma wrote: Dear Gromacs users, I have to simulate a system consisting of Protein+MG+GDP where Protein is in complex with MG and GDP. I generated the GDP parameters using antechamber and then converted the topology,coordinate and parameter files to the corresponding gromacs format. Then, I tried to start with the simulation using AMBER ff03 forcefield. The system ran well till energy minimization step, but at equilibration steps it is showing lincs error at NVT equilibration step. What was the output of energy minimization? What I'm looking for is the actual screen output with Epot and Fmax. Just because EM completed does not mean it was necessarily sufficient. I used 2 coupling groups for my system with lincs constraint algorithm as follows: *tc-grps = Protein_MG_GDP Water_and_ions * I tried turning off lincs warning too, den NVT equilibration was done finely but the system was blowing up during NPT equilibration. I tried No, NVT was not fine - you ignored a major error that indicates instability in your system. with 3-4 steps of minimization also, but it didnt work (I have tried with lincs warning off in NPT too). I have visualized the NVT output trajectory and compared it with the initial structure too, and the trajectory was fine. You'll have to define what you think fine means, because if the simulation can only run when disabling LINCS warnings, something has to be severely wrong. I am unable to figure out the reason for why the system is blowing up. I am following the drug-ligand simulation tutorial but still can't figure out the problem. Can anyone suggest any possible means to overcome this situation? Yes, a general workflow is here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System The source of the error could be any number of things, including incorrect topology, unsuitable .mdp settings, inappropriate system construction/minimization, or any combination of those factors. Posting a complete .mdp file would be helpful. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nrexcl = 2 or 3?
On 15/12/11, lq z lqz@gmail.com wrote: Dear GMXers, I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3? Whatever value pdb2gmx generates for CHARMM, probably 3. According to the manual (v 4.5), nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away. In charmm ff, 1-4 interactions are needed and it is no further than 3 bonds away, ... but 1-4 interactions are regarded as bonded interactions. so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately. By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have charges. If I use nrexcl =3, no electrostatics energy is reported while the value matches with the one calculated by hand when I set nrexcl to be 2. As expected. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to use g_dipoles
On 15/12/11, 李浩 liha...@gmail.com wrote: dear users: I am using Gromacs 4.0.5. My system consist of chared plain and charged protein. How can i use the g_dipoles to get the protein's dipole? what is the exact option? Start with g_dipoles -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nrexcl = 2 or 3?
Hi Mark, I do not quite understand. For example, in amber ff, 1-4 interactions (except the part from dihedral interactions) are calculated according to non-bonded parameters and then scaled by 1/2 or 5/6. When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using non-bonded parameters? Thanks, Yun On Wed, Dec 14, 2011 at 4:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 15/12/11, *lq z *lqz@gmail.com wrote: Dear GMXers, I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3? Whatever value pdb2gmx generates for CHARMM, probably 3. According to the manual (v 4.5), nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away. In charmm ff, 1-4 interactions are needed and it is no further than 3 bonds away, ... but 1-4 interactions are regarded as bonded interactions. so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately. By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have charges. If I use nrexcl =3, no electrostatics energy is reported while the value matches with the one calculated by hand when I set nrexcl to be 2. As expected. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nrexcl = 2 or 3?
On 15/12/11, Yun Shi yunsh...@gmail.com wrote: Hi Mark, I do not quite understand. For example, in amber ff, 1-4 interactions (except the part from dihedral interactions) are calculated according to non-bonded parameters and then scaled by 1/2 or 5/6. Yes, see discussion of gen-pairs in manual section 5.7.1 When setting nrexcl = 3, which is the default, aren't 1 - 4 interactions excluded from using non-bonded parameters? This is a separate mechanism. Exclusions for non-bonded interactions are applied on the fly in mdrun. That doesn't apply to 1-4 parameter generation, but it is necessary for the set of choices of nrexcl, gen-pairs, fudgeXX, [atomtypes], [nonbond_params], [pairtypes] and [pairs] to be consistent. Details vary with the particular force field. Parameters for bonded 1-4 interactions (a.k.a. pairs) are generated in grompp according to the rules of the force field - either from the [pairtypes], [pairs] or from scaling depending on the force field and interaction type. Mark Thanks, Yun On Wed, Dec 14, 2011 at 4:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 15/12/11, lq z lqz@gmail.com wrote: Dear GMXers, I need to use charmm ff (same question for amber ffs), and am confused with what value I should give to nrexcl in [ moleculetype ], 2 or 3? Whatever value pdb2gmx generates for CHARMM, probably 3. According to the manual (v 4.5), nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away. In charmm ff, 1-4 interactions are needed and it is no further than 3 bonds away, ... but 1-4 interactions are regarded as bonded interactions. so I should use nrexcl = 2. However, it is 3 in charmm27.ff/ folder. Yes, CHARMM has special parameters for some 1-4 interactions, which are dealt with seperately. By the way, I did a simple test with a dihedral a-b-c-d. Only a and d have charges. If I use nrexcl =3, no electrostatics energy is reported while the value matches with the one calculated by hand when I set nrexcl to be 2. As expected. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MD simulation of Glycoproteion
Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? Any suggestions? That's all. Thank you-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Glycoproteion MD
Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MD simulation of Glycoproteion
Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? Any suggestions? That's all. Thank you-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD simulation of Glycoproteion
2011/12/14 陈应广 525342...@qq.com ** Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? *Any suggestions? * I guess you have to check the residue names, especially those glyco parts, which are probably not in the force field you chose. ** That's all. Thank you ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
回复： [gmx-users] MD simulation of Glycoproteion
Thank your advance I have check the residue names, in glyco parts, it contain:NLN,2MA,6MA,WMB,4YB,0YB,XMA,0MA and so on.and I found the define of the residue ,but the format of the define isn't adopt to the Gromacs 's .rtp file. now I don't know how to do it, who can help me? thanking all -- 原始邮件 -- 发件人: Yun Shiyunsh...@gmail.com; 发送时间: 2011年12月15日(星期四) 上午10:48 收件人: Discussion list for GROMACS usersgmx-users@gromacs.org; 主题: Re: [gmx-users] MD simulation of Glycoproteion 2011/12/14 陈应广 525342...@qq.com Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? Any suggestions? I guess you have to check the residue names, especially those glyco parts, which are probably not in the force field you chose. That's all. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD simulation of Glycoproteion
On 15/12/2011 1:05 PM, ??? wrote: Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. So check out http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database like it probably suggested. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? /Any suggestions? / That's all. Your literature searching for similar published work should probably have suggested some good options. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: submission error
Hi, When i tried running mdrun without mip i received the same error ie when i gave mdrun -deffnm md i got= Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.4 (single precision) Loaded with Money p0_23443: p4_error: interrupt SIGx: 4 Thanks, Aiswarya On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Please anyone can help with this error. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: submission error
On 15/12/2011 4:51 PM, aiswarya pawar wrote: Hi, When i tried running mdrun without mip i received the same error ie when i gave mdrun -deffnm md i got= Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file md.tpr, VERSION 4.5.4 (single precision) Loaded with Money p0_23443: p4_error: interrupt SIGx: 4 The job you ran below with poe did not have the MPI suffix, so I am not convinced you are doing appropriate things with appropriate executables. Above, a p4_error is consistent with an MPI-enabled executable. Get an MPI hello world program and get it running before worrying about GROMACS. Follow the user guide for your cluster. Get your MPI-enabled mdrun suffixed with _mpi like the installation guides recommend. Mark Thanks, Aiswarya On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi users, I have a submission script for gromacs mdrun to be used on IBM cluster, but i get an error while running it. the script goes like this= #!/bin/sh # @ error = job1.$(Host).$(Cluster).$(Process).err # @ output = job1.$(Host).$(Cluster).$(Process).out # @ class = ptask32 # @ job_type = parallel # @ node = 1 # @ tasks_per_node = 4 # @ queue echo _ echo LOADL_STEP_ID=$LOADL_STEP_ID echo _ machine_file=/tmp/machinelist.$LOADL_STEP_ID rm -f $machine_file for node in $LOADL_PROCESSOR_LIST do echo $node $machine_file done machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l` echo $machine_count echo MachineList: cat /tmp/machinelist.$LOADL_STEP_ID echo _ unset LOADLBATCH env |grep LOADLBATCH cd /home/staff/1adf/ /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID rm /tmp/machinelist.$LOADL_STEP_ID i get an out file as= _ LOADL_STEP_ID=cnode39.97541.0 _ 4 MachineList: cnode62 cnode7 cnode4 cnode8 _ p0_25108: p4_error: interrupt SIGx: 4 p0_2890: p4_error: interrupt SIGx: 4 p0_2901: p4_error: interrupt SIGx: 15 p0_22760: p4_error: interrupt SIGx: 15 an error file = Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision) Sorry couldn't backup /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# Back Off! I just backed up /home/staff/1adf/md.log to /home/staff/1adf/#md.log.14# ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 0 Please anyone can help with this error. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: calculation of standard deviation of SASA per residue
Hi Mark, Thank you very much for your help. I got my answer. I chose protein as the group for calculating SASA and residue1 for output and i got the SASA of residue 1 vs time. This gave me the correct mean SASA of residue1 and also its std deviation. I repeated the same way for all the residues and got SASA per residue with std deviation of each. Thanks again!! Regards, Harpreet On 14/12/2011 4:01 PM, Harpreet Basra wrote: Hi I want to calculate the standard deviation of SASA of each residue of a peptide. When using -or option for complete peptide in g_sas we get residue vs sasa only. I don't follow what result you are describing as unsuitable for you needs. So i tried by creating an index file for each residue separately (residue1.ndx, residue2.ndx and so forth) and then by calculating by using -o option i got time vs sasa for each residue, thinking that this will give me average sasa per residue as well as its standard deviation. But I see that the average value obtained by this method for each residue is different from the one i got by using -or option (and calculating for complete peptide). Why is it so? Doesnt -or option gives average sasa over entire trajectory per residue? Can anyone suggest any way to compute the standard deviation? It's hard to comment when we don't know which groups you chose for which calculation. Using an index file to change *only* the output group and using g_sas -or should definitely work, but I don't see why custom groups should be needed at all. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] calculation of density for martini coarse-grained
Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, but about density, I think that I am wrong: 151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ), then 755 * 72 amu = 54360 amu, and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!! And there is the same problem after adding water and ion! May I know my mistake, Please? 2- My surfactant molecule has one positive charge, after I added 151 surfactants, water and antifreezewater, Gromacs answer me that (for each step): NOTE1: system has non-zero total charge: 1.51e+2 Then I added 151 ions to my system with -nn 151 for neutralization, but in the genion.log was reported that System total charge: 151.000!!!, but after doing grompp, GROMACS didn't report note about system charge. Is this right? Please help me. Best Regards Sara-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculation of density for martini coarse-grained
On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, but about density, I think that I am wrong: 151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ), then 755 * 72 amu = 54360 amu, and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!! Please use standard abbreviations for your units unless you want risk people not taking you seriously... I've no idea how you can divide 90254.026*10e-24 by 1000*10e-24 and get 52.23 or 15.8111 And there is the same problem after adding water and ion! May I know my mistake, Please? 2- My surfactant molecule has one positive charge, after I added 151 surfactants, water and antifreezewater, Gromacs answer me that (for each step): NOTE1: system has non-zero total charge: 1.51e+2 Then I added 151 ions to my system with -nn 151 for neutralization, but in the genion.log was reported that System total charge: 151.000!!!, When did genion report that, before or after adding ions? Did the addition succeed? Are your solvent molecules named SOL? but after doing grompp, GROMACS didn't report note about system charge. Is this right? We don't know. Copied and pasted command lines and terminal output are a lot more useful for getting help than sentences describing them. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
