[gmx-users] can extract edr and cpt of one frame?
Hi, I want extract one frame from NPT to run MD because for md need npt.gro and npt.cpt So, if can we extract cpt of one frame? and because I want to check if this frame at equilibration state, use g_energy -f npt.edr So, if can we extract edr of one frame? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/can-extract-edr-and-cpt-of-one-frame-tp5009322.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] GROMACS on GPU
Dear gromacs users, Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option -testverlet to mdrun in order to run it on GPU, it returns error nonbond potiential is not supported. Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance! Yeping Sun -- 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] gromacs on GPU
Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option -testverlet to mdrun in order to run it on GPU, it returns error nonbond potiential is not supported. Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance! integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-SwitchTcoupl = v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 1nstenergy = 5000energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes Yeping Sun -- 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] can extract edr and cpt of one frame?
On Fri, Jun 21, 2013 at 8:19 AM, maggin maggin.c...@gmail.com wrote: Hi, I want extract one frame from NPT to run MD because for md need npt.gro and npt.cpt So, if can we extract cpt of one frame? No. A checkpoint file has only one frame, as you can see with gmxcheck or gmxdump. and because I want to check if this frame at equilibration state, use g_energy -f npt.edr So, if can we extract edr of one frame? You can extract an frame using eneconv and trjconv (see their -h) and give those to grompp. Mark Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/can-extract-edr-and-cpt-of-one-frame-tp5009322.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] gromacs on GPU
On Fri, Jun 21, 2013 at 8:33 AM, sunyep...@aliyun.com wrote: Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option -testverlet to mdrun in order to run it on GPU, it returns error nonbond potiential is not supported. Please copy and paste actual error messages, not what you think was important about it. -testverlet is not an all-purpose magic bullet, and there are algorithm combinations that are implemented differently in the group and verlet schemes. See manual 7.3.10-11 Mark Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance! integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-SwitchTcoupl = v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 1nstenergy = 5000energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes Yeping Sun -- 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] free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
Hi gmx-users, I almost reproduced free energy calculations of methane in water on Justin's website. First of all, I am able to follow the workflow of computing solvation free energy for several times with Gromacs version 4.5.7 and version 4.6.2 installed in two identical Linux boxes. However. the output results of GMX ver 4.5.7 and ver 4.6.2 show different values of dG ## GMX Ver. 4.5.7: lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.01 +/- 0.00 lambda 0.100 - 0.150, DG -0.03 +/- 0.01 lambda 0.150 - 0.200, DG -0.08 +/- 0.00 lambda 0.200 - 0.250, DG -0.15 +/- 0.00 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.28 +/- 0.00 lambda 0.350 - 0.400, DG -0.38 +/- 0.00 lambda 0.400 - 0.450, DG -0.50 +/- 0.01 lambda 0.450 - 0.500, DG -0.66 +/- 0.01 lambda 0.500 - 0.550, DG -0.90 +/- 0.01 lambda 0.550 - 0.600, DG -1.21 +/- 0.01 lambda 0.600 - 0.650, DG -1.37 +/- 0.01 lambda 0.650 - 0.700, DG -1.25 +/- 0.01 lambda 0.700 - 0.750, DG -0.96 +/- 0.00 lambda 0.750 - 0.800, DG -0.62 +/- 0.00 lambda 0.800 - 0.850, DG -0.31 +/- 0.00 lambda 0.850 - 0.900, DG -0.03 +/- 0.00 lambda 0.900 - 0.950, DG 0.20 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.31 +/- 0.04 ## GMX ver. 4.6.2 ver point 0.000 - 0.050, DG 0.00 +/- 0.00 point 0.050 - 0.100, DG -0.03 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.14 +/- 0.00 point 0.200 - 0.250, DG -0.20 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.34 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.54 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.01 point 0.550 - 0.600, DG -1.24 +/- 0.02 point 0.600 - 0.650, DG -1.39 +/- 0.02 point 0.650 - 0.700, DG -1.28 +/- 0.01 point 0.700 - 0.750, DG -1.00 +/- 0.00 point 0.750 - 0.800, DG -0.67 +/- 0.00 point 0.800 - 0.850, DG -0.36 +/- 0.00 point 0.850 - 0.900, DG -0.09 +/- 0.00 point 0.900 - 0.950, DG 0.14 +/- 0.00 point 0.950 - 1.000, DG 0.33 +/- 0.00 total 0.000 - 1.000, DG -9.23 +/- 0.03 ## The value of DG (= -9.23 kJ mol -1) by GMX ver 4.6.2 is very close to that by Justin or Shirts et.al of 2.24 kcal mol-1 (~ -9.36 kJ mol -1), while that of GMX ver 4.5.7 ( =-8.31 kJ mol-1) is far away. I wonder if someone has similar experience to explain the inconsistency between the outputs from ver 4.5.7 (~-8.31 kJmol-1) and ver 4.6.2 (-9.23 kJmol-1 ), despite the values of dG computed by others. Second, the reason why I almost reproduced dG but not completely is because I removed the step of L- BFGS minimization. I was not able to pass this step for both GMX versions. Here shows the warning. Fatal error: The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent). L-BFGS mdp file can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_l-bfgs.mdp Again, I appreciate advice or a hint. Thanks, Dwey -- 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: Test Particle Insertion
Dear Rajesh and Damas, Thank you for your help. I will try now. Thanks again. Sincerely, Anh -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of gmx-users-requ...@gromacs.org Sent: Thursday, June 20, 2013 10:19 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 110, Issue 115 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Decouple (Justin Lemkul) 2. Re: Test Particle Insertion (Jo?o M. Damas) 3. Re: Decouple (Justin Lemkul) 4. (no subject) (Hari Pandey) 5. Re: (no subject) (Justin Lemkul) -- Message: 1 Date: Thu, 20 Jun 2013 17:16:29 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Decouple To: Hari Pandey hariche...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51c3712d.5030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 6/20/13 5:01 PM, Hari Pandey wrote: Hi , How do I solve this problem in GROMACS: I have a system with 3 part A,B and C I have to put thermostat for A and C but not for B. Gromacs display error, what is temperature for B. How do aI decouple part B Per the manual: tau-t: [ps] time constant for coupling (one for each group in tc-grps), -1 means no temperature coupling -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 2 Date: Fri, 21 Jun 2013 00:29:15 +0100 From: Jo?o M. Damas jmda...@itqb.unl.pt Subject: Re: [gmx-users] Test Particle Insertion To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAN8VxHxcUPN6Q0fTjRURD0e0vjzP-2uzqODBL_NhHLDdt=4...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear Anh, You need to construct a .tpr file for the mdrun -rerun with: - a .gro file with the ligand to be inserted at the end, which _must_ be geometrically centered at 0,0,0 ; - a matching .top file (which means with the ligand topology appropriately inserted) ; - a .mdp file with the specific parameters for the tpi algorithm . Since you happen to have a single particle to insert, that particle's coordinates should be 0,0,0 in the .gro file from grompp (your initial.gro). Best, Jo?o On Thu, Jun 20, 2013 at 8:08 PM, Phan, Anh T. anhp...@ou.edu wrote: Dear GMX Users, My name is Anh Phan, a PhD student at University of Oklahoma. I would like to calculate excess chemical potential of one gas molecule in water solvent using Widom test particle insertion with Gromacs. In this method, I will insert this gas molecule at a random position in each configuration of the system. With Gromacs, I see I can use tpi (integrator = tpi). I know I have to add this gas molecule in the topology (topol.top) Also, it is indicated in the manual that insertions are performed nsteps times in each frame at random locations and with random orientiations of the molecule. That is what I desire. The question I would like to ask is whether I have to add the specified coordinate of gas molecule in the .gro file at the beginning of running simulation. For example, in the initial.gro file . 26734SOL OW45744 21.969 6.237 2.921 26734SOLHW145745 21.969 6.253 3.019 26734SOLHW245746 21.886 6.188 2.895 26735SOL OW45747 15.155 7.211 2.853 26735SOLHW145748 15.220 7.265 2.801 26735SOLHW245749 15.204 7.151 2.916 26736SOL OW45750 24.606 4.896 3.053 26736SOLHW145751 24.594 4.972 2.989 26736SOLHW245752 24.532 4.896 3.120 26737INS X457521.0001.0001.000 ( Do I have to add this line in the initial.gro file) The command lines grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr -maxwarn 2 mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg I am looking forward to receiving your reply. Thank you for your help. Sincerely, Anh -- 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
Re: [gmx-users] free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
On 6/21/13 11:07 AM, Dwey wrote: Hi gmx-users, I almost reproduced free energy calculations of methane in water on Justin's website. First of all, I am able to follow the workflow of computing solvation free energy for several times with Gromacs version 4.5.7 and version 4.6.2 installed in two identical Linux boxes. However. the output results of GMX ver 4.5.7 and ver 4.6.2 show different values of dG ## GMX Ver. 4.5.7: lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.01 +/- 0.00 lambda 0.100 - 0.150, DG -0.03 +/- 0.01 lambda 0.150 - 0.200, DG -0.08 +/- 0.00 lambda 0.200 - 0.250, DG -0.15 +/- 0.00 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.28 +/- 0.00 lambda 0.350 - 0.400, DG -0.38 +/- 0.00 lambda 0.400 - 0.450, DG -0.50 +/- 0.01 lambda 0.450 - 0.500, DG -0.66 +/- 0.01 lambda 0.500 - 0.550, DG -0.90 +/- 0.01 lambda 0.550 - 0.600, DG -1.21 +/- 0.01 lambda 0.600 - 0.650, DG -1.37 +/- 0.01 lambda 0.650 - 0.700, DG -1.25 +/- 0.01 lambda 0.700 - 0.750, DG -0.96 +/- 0.00 lambda 0.750 - 0.800, DG -0.62 +/- 0.00 lambda 0.800 - 0.850, DG -0.31 +/- 0.00 lambda 0.850 - 0.900, DG -0.03 +/- 0.00 lambda 0.900 - 0.950, DG 0.20 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.31 +/- 0.04 ## GMX ver. 4.6.2 ver point 0.000 - 0.050, DG 0.00 +/- 0.00 point 0.050 - 0.100, DG -0.03 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.14 +/- 0.00 point 0.200 - 0.250, DG -0.20 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.34 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.54 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.01 point 0.550 - 0.600, DG -1.24 +/- 0.02 point 0.600 - 0.650, DG -1.39 +/- 0.02 point 0.650 - 0.700, DG -1.28 +/- 0.01 point 0.700 - 0.750, DG -1.00 +/- 0.00 point 0.750 - 0.800, DG -0.67 +/- 0.00 point 0.800 - 0.850, DG -0.36 +/- 0.00 point 0.850 - 0.900, DG -0.09 +/- 0.00 point 0.900 - 0.950, DG 0.14 +/- 0.00 point 0.950 - 1.000, DG 0.33 +/- 0.00 total 0.000 - 1.000, DG -9.23 +/- 0.03 ## The value of DG (= -9.23 kJ mol -1) by GMX ver 4.6.2 is very close to that by Justin or Shirts et.al of 2.24 kcal mol-1 (~ -9.36 kJ mol -1), while that of GMX ver 4.5.7 ( =-8.31 kJ mol-1) is far away. I wonder if someone has similar experience to explain the inconsistency between the outputs from ver 4.5.7 (~-8.31 kJmol-1) and ver 4.6.2 (-9.23 kJmol-1 ), despite the values of dG computed by others. I can't explain the difference you are seeing, but I know the results have been reproduced with versions 4.5.3 and 4.5.5. It is good to know that the latest version (4.6.2) is working as expected, but it might be useful to figure out what's up with 4.5.7. Please let me know if you can reproduce the right result with 4.5.5. Second, the reason why I almost reproduced dG but not completely is because I removed the step of L- BFGS minimization. I was not able to pass this step for both GMX versions. Here shows the warning. Fatal error: The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent). L-BFGS mdp file can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_l-bfgs.mdp Add define = -DFLEXIBLE to the .mdp file. Water molecules are constrained via SETTLE, so that causes issues with L-BFGS. When I designed the tutorial, grompp did not do that check, so it was ignoring those constraints and silently moving past it. I will fix the .mdp file. Thanks for bringing that to my attention. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Tempereture coupling and heat flux on each part
Hi all gromacs users, I am new to GROMACS , please help me I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. In gromacs I want to do Following: 1: A B temperature coupling 2: C not coupling, Free to increase or decrease temperature from its initial temperature 500K 3: after steady state want to get the final temperature of the part C 4: Calculate Heat flux on each part after 100 ps. I used tau_t =-1 for part C but wandering, is it sufficient to keep tau_t =-1 for avobe work? Thanks for your help for that My NVT.mdp is: ; simulation at 300K and 2 ps is on constraints =all-bonds integrator =md dt =0.001 ; ps nsteps =10 ; total 100 ps nstcomm =10 nstxout =1000 nstxtcout =0 nstvout =0 nstfout =0 nstenergy =100 nstlist =100 ns_type =grid rlist =0.5 coulombtype =pme rcoulomb =0.5 vdwtype =cut-off rvdw =0.5 pme_order =4 ewald_rtol =1e-5 optimize_fft =yes DispCorr =no ;Brendsen tempereture coupling is on Tcoupl = nose-hoover tau_t =0.001 -1 0.001 tc-grps =A B C ref_t =750 300 350 ;pressure coupling is on Pcoupl =no Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =yes gen_temp =750 300 350 gen_seed =-1 MY NPT.mdp is: ( here all output control parameters also) ;Brendsen tempereture coupling is on Tcoupl =nose-hoover tau_t =1 -1 1 tc-grps =NCALPHA MIDDLE NCNN ref_t =750 300 350 ;pressure coupling is on Pcoupl =Berendsen Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =1 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no gen_temp =750 300 350 gen_seed =-1 MY NVE.mdp is: ( here all output control parameters also) tc-grps = A B C ref_t =750 300 300 energygrps = NCALPHA MIDDLE NCNN tcoupl = nose-hoover tau-t = 1 -1 1 ;pressure coupling is on Pcoupl =no ;Pcoupltype =isotropic ;tau_p =0.5 ;compressibility =1e-5 ;ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no ; gen_temp =750 300 350 ; gen_seed =-1 What I did is: pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; mdrun -deffnm em -v; grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; mdrun -deffnm nvt -v; grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; mdrun -deffnm npt -v grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; mdrun -deffnm nve -v; g_energy -f nve.edr -s nve.tpr -o F1.xvg Thanks for your help -- 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
