[gmx-users] problem with gromcas 4.5.3
I have installed gromacs version 4.5.3. when I want to use pdb2gmx for generating .top and .gro files for 1000 argon atoms, in topology file I have seen another atom O with mass 1.48594e-41 as below I do not know what to do.I do not confront with such problems when I had 4.0.7 version of gromacs. please help me. also I have used gromos43a1 force feild. [ moleculetype ] ; Namenrexcl Other_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GAS rtp GAS q 0.0 1 AR 1GAS AR 1 0 1 ; qtot 0 ; residue 2 GAS rtp GAS q 0.0 2 O 2GAS AR 2 0 1.48594e-41 ; qtot 0 ; residue 3 GAS rtp GAS q 0.0 3 O 3GAS AR 3 0 1.48594e-41 ; qtot 0 ; residue 4 GAS rtp GAS q 0.0 4 O 4GAS AR 4 0 1.48594e-41 ; qtot 0 ; residue 5 GAS rtp GAS q 0.0 5 O 5GAS AR 5 0 1.48594e-41 ; qtot 0 ; residue 6 GAS rtp GAS q 0.0 6 O 6GAS AR 6 0 1.48594e-41 ; qtot 0 ; residue 7 GAS rtp GAS q 0.0 -- 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] problem with gromcas 4.5.3
leila separdar wrote: I have installed gromacs version 4.5.3. when I want to use pdb2gmx for generating .top and .gro files for 1000 argon atoms, in topology file I have seen another atom O with mass 1.48594e-41 as below I do not know what to do.I do not confront with such problems when I had 4.0.7 version of gromacs. please help me. also I have used gromos43a1 force feild. Sounds like it's related to (or the same as) a known issue: http://redmine.gromacs.org/issues/618 Note that, for a monoatomic species (or any single molecule, really) pdb2gmx is not necessary. Writing a simple argon.itp containing the one atom and its nonbonded parameters is very trivial, since there aren't even any bonded parameters to assign, just a single [atoms] directive. Then just #include it in your .top. -Justin [ moleculetype ] ; Namenrexcl Other_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GAS rtp GAS q 0.0 1 AR 1GAS AR 1 0 1 ; qtot 0 ; residue 2 GAS rtp GAS q 0.0 2 O 2GAS AR 2 0 1.48594e-41 ; qtot 0 ; residue 3 GAS rtp GAS q 0.0 3 O 3GAS AR 3 0 1.48594e-41 ; qtot 0 ; residue 4 GAS rtp GAS q 0.0 4 O 4GAS AR 4 0 1.48594e-41 ; qtot 0 ; residue 5 GAS rtp GAS q 0.0 5 O 5GAS AR 5 0 1.48594e-41 ; qtot 0 ; residue 6 GAS rtp GAS q 0.0 6 O 6GAS AR 6 0 1.48594e-41 ; qtot 0 ; residue 7 GAS rtp GAS q 0.0 -- 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] PROCHEK-NMR instalation problem
hi all Anybody guide me in installig the PROCHECK software and how to run it ?? best regards -- 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] PROCHEK-NMR instalation problem
najwa drici wrote: hi all Anybody guide me in installig the PROCHECK software and how to run it ?? This list is for Gromacs-related questions. Consult whatever documentation Procheck provides and make use of whatever support resources they offer. -Justin best regards -- 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] excess chemical potential
Hello, I want to calculate the excess chemical potential of one dissolved molecule within an liquid system. The excess chemical potential should be delta G. The equation for delta G is given in manual: With -fee an estimate is calculated for the free-energy difference with an ideal gas state: Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln e(Upot/kT) What is the meaning of this Upot? Does it describe the interaction energy of the dissolved gas what I need for the calculations. Or do I need the two values for delta G with 1 molecule gas and without it to calculate the Henry constant with delta G? Regards, Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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] ***Extended deadline: March 18*** COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - Call for Papers
Please note submission deadline extended to March 18, 2011 (apologies if you receive multiple copies of this call for papers) # IEEE WETICE 2011 2nd International Track on Collaborative Modeling and Simulation CALL FOR PAPERS # June 27 - June 29, 2011, Paris (France) http://www.sel.uniroma2.it/CoMetS11 # # Papers Due: *** March 18, 2011 *** EXTENDED # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. # Modeling and Simulation (MS) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, MS is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of MS activities increases for the more complex models and for the communications among a wider number and variety of MS stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of MS activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among MS stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to MS activities, the track seeks innovative contributions that deal with the application of MS practices to the design of collaborative environments. These environments are continuously becoming more complex, and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. MS offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non–exhaustive list of topics of interest includes: * collaborative environments for MS * collaborative Systems of Systems MS * workflow modelling for collaborative environments and processes * agent-based MS * collaborative distributed simulation * collaborative component-based MS * net-centric MS * web-based MS * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environments * domain specific languages for collaborative MS * databases and repositories for MS * distributed virtual environments * virtual research environment for MS To stimulate creativity, however, the track maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and MS. +++ On-Line Submissions and Publication +++ CoMetS'11 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the track research area. Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Accepted full papers will be included in the proceedings and published by the IEEE Computer Society Press (IEEE approval pending). Please note that at least one author for each accepted paper should register to attend WETICE 2011 to have the paper published in the proceedings. Authors may contact the organizers for expression of interests and content appropriateness at any time. Papers can be submitted in PDF format at the submission site (https://www.easychair.org/conferences/?conf=comets2011), which is supported by the EasyChair conference management system. Please contact the track chairs (comets2...@easychair.org) if you experience problems with the EasyChair Web site. +++ Important Dates
[gmx-users] Positive potential energy in simulation using polarizable model
Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a positive value for the potential energy? In my simulation, for every step, the system is energy minimized in order to accommodate the behavior of the shell particles. For the shell particles, I use emtol = 0.1 and niter = 100. In the log file, the potential energies are mostly reported as positives (except in the beginning steps), but there is no line saying that the 'energy minimization (EM) does not converge'. I understand that if the potential energy is positive, this may indicate that the system is exploding. When I calculate the density, however, it corresponds quite well. Many thanks in advance. Regards, Aldi -- 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] Positive potential energy in simulation using polarizable model
On 2011-02-27 21.20, aldi asmadi wrote: Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a positive value for the potential energy? In my simulation, for every step, the system is energy minimized in order to accommodate the behavior of the shell particles. For the shell particles, I use emtol = 0.1 and niter = 100. In the log file, the potential energies are mostly reported as positives (except in the beginning steps), but there is no line saying that the 'energy minimization (EM) does not converge'. I understand that if the potential energy is positive, this may indicate that the system is exploding. When I calculate the density, however, it corresponds quite well. Many thanks in advance. Regards, Aldi You should subtract the energy of a monomer in order to get the intermolecular energy. Try computing the heat of vaporization: DHvap = Epot(g) - Epot(l) + kBT and compare it to the experimental value. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Positive potential energy in simulation using polarizable model
Many thanks David. Just want to confirm that I understand how to calculate the monomer correctly. So I put the single molecule inside a large cubic box, say with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the same cut-off parameters as the ones that I apply during my bulk simulation? On Sun, Feb 27, 2011 at 11:34 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-02-27 21.20, aldi asmadi wrote: Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a positive value for the potential energy? In my simulation, for every step, the system is energy minimized in order to accommodate the behavior of the shell particles. For the shell particles, I use emtol = 0.1 and niter = 100. In the log file, the potential energies are mostly reported as positives (except in the beginning steps), but there is no line saying that the 'energy minimization (EM) does not converge'. I understand that if the potential energy is positive, this may indicate that the system is exploding. When I calculate the density, however, it corresponds quite well. Many thanks in advance. Regards, Aldi You should subtract the energy of a monomer in order to get the intermolecular energy. Try computing the heat of vaporization: DHvap = Epot(g) - Epot(l) + kBT and compare it to the experimental value. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive potential energy in simulation using polarizable model
On 2011-02-27 21.49, aldi asmadi wrote: Many thanks David. Just want to confirm that I understand how to calculate the monomer correctly. So I put the single molecule inside a large cubic box, say with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the same cut-off parameters as the ones that I apply during my bulk simulation? Infinite cutoff is best, since you probably use PME in bulk but can not do that in gas phase. If you are using the Charmm parameters I'm pretty sure they have published DHvap values so you can compare. On Sun, Feb 27, 2011 at 11:34 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-02-27 21.20, aldi asmadi wrote: Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a positive value for the potential energy? In my simulation, for every step, the system is energy minimized in order to accommodate the behavior of the shell particles. For the shell particles, I use emtol = 0.1 and niter = 100. In the log file, the potential energies are mostly reported as positives (except in the beginning steps), but there is no line saying that the 'energy minimization (EM) does not converge'. I understand that if the potential energy is positive, this may indicate that the system is exploding. When I calculate the density, however, it corresponds quite well. Many thanks in advance. Regards, Aldi You should subtract the energy of a monomer in order to get the intermolecular energy. Try computing the heat of vaporization: DHvap = Epot(g) - Epot(l) + kBT and compare it to the experimental value. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing your message to the list and would ask that all further discussion be sent there. See comments below. Yanping Fan, Liza (Dr) wrote: Dear Justin: Good day. I found your comments in gmx-user communications. And you are very experienced in GMX. I’m using gmx 453 now, with DNA system. Pdb2gmx is ok, but gmx treated each string as protein. I used command What do you mean treated each string as protein? DNA residues are defined in residuetypes.dat as such, so I don't know how DNA residues would be interpreted as protein by any tool. In principle, there is no problem with this interpretation, as long as the parameters are assigned correctly. The .pdb file you sent me contains both protein and DNA, so I suspect that nothing is wrong; you have some residues that are DNA and others that are protein. You don't say which tool is treating your DNA as protein, but I would encourage you to check the output carefully. If you still suspect something is wrong, please provide useful diagnostic information (i.e., the tool reporting the potential problem and the output it is giving you that leads you to suspect a problem). pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p then choose charmm27 ff, everything looks good. However I found during my md runs, DNA separated. System goes to weird. Do I need to remove TER between the paired stands? I attached pdb file for your reference. Thank you very much for your guildance. There is probably not separation, just a periodicity effect. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin Best regards, Liza CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- 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] .tdr file not created
hi I installed gromacs through the synaptics package manager in ubuntu 10.10 Since I am new to linux. So after installation when I tried to run the example tutorials available in tutor folder, its not running. When I tried to run the program water the .tdr file is not created while executing the grompp -v command, and only a .mdp file is created. So is this the problem with the installation or some other problem.Since .tdr file is missing gmxdump is not working. -- 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] about -CN triple bond
Hi, I try to add a dummy atom in my small molecular pdb and topology file. (attached files) But the MDS process still shut down. The msg. is [1]+ Exit 255nohup mdrun -v -deffnm npt_cmplx Could you give me some suggestions for dealing with the problem. Thaks a lot. Best, Chia-yun Chang 2011/2/19 Mark Abraham mark.abra...@anu.edu.au On 19/02/2011 5:18 PM, C.Y. Chang wrote: Hi, The errpr msg. that I expressed in the previous mail is unclear. It really happened in the grompp step of my dealinw with the em. The manual shows that the viste can be used by [ virtual sites2 ] That's misspelled too. Underscores are significant. You have to be literal when dealing with computers. ; Site from funct a 5 1 2 1 0.7439756 What should I choose the vsite for the -CN group? (2, 3fd or others?) The problems come when the force from normal angle and dihedral functions aren't numerically stable when there are 3 collinear atoms. The way to avoid this is to have one of those atoms virtual. Forces on it get projected onto the real atoms from which it is defined, the integration of forces proceeds only on the real atoms, and the position of the virtual site gets reconstructed later. So, which type do you think will work best here? I read the manual and the columns of the vsite need some parameters. The Site seems to be the atom number. Yes. The from seems some atom group, but which atoms should be included? The real atoms that form the virtual site. The number and order depends on the type of virtual site. Which atom is which is covered back in 4.7 You need to read that together with 5.2.2, like I said several emails ago. How could obtain the func values? That's situation-dependent. Here, you want to pick a position along the line that will lead to the three atoms being a sensible distance apart. Could you give me a molecule for my example? No, I don't have one. Your example above will construct atom 5 from 1 and 2 75% of the way along the line from 1 to 2, per Figure 4.16 and equation 4.134. Mark Thanks for your help. Best, Chia-yun 2011/2/19 Mark Abraham mark.abra...@anu.edu.au On 19/02/2011 3:02 PM, C.Y. Chang wrote: Hi, I have tried to add [ position restraints ] This is misspelled. Surely grompp warned about this? 2 1 1000 1000 1000 ; Restrain to a point 1 1 1000 0 1000 ; Restrain to a line (Y-axis) 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane) in the end of the topology file. This does not even approach the solution to your problem. Position restraints inhibit diffusion and structural changes. You need a vsite, like you knew earlier. In the em. process, I get the eroor msg. No, this error happened in grompp. Fatal error: Invalid dihedral type 1000 GROMACS didn't recognise the mis-spelled directive, and so it's trying to make sense of your position restraint lines as dihedrals. Mark Chia-yun 2011/2/18 Mark Abraham mark.abra...@anu.edu.au On 18/02/2011 1:13 PM, C.Y. Chang wrote: Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The vsite has been mentioned, and I have refered to the gromacs manual. But I don't understand that how I can use the vsite. The theory is discussed in chapter 4 and there's a brief example in 5.2.2. What have you tried and what went wrong? Mark (add the toplogy file or use the command line?) I attach the PDB and toplogy file of the molecule. First, I performed the molecular dynamic simulation for the pure lipid bilayer, and the step was been finished. After I insert the molecule, these command lines are performed. grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr mdrun -v -deffnm em grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr nohup mdrun -v -deffnm npt_cmplx Thanks for your help. Best, Chia-yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list
