[gmx-users] Cross-correlation map of protein residues
Dear list, I am looking for a gromacs tool which is able to calculate/draw a map of residues which are either in their motion correlated or anti correlated. first i thought i could just use g_covar with c-alpha and use the -xpma option but while reading previous mailing list posts people said that the atomic covariance matrix does not correlate motions. All posts I found where older and the script from the gromacs site for a g_covar tool which can calculate the correlation plot is from 2009. Therefore, i wanted to know if gromacs 5 is able to directly calculate the plot. if not does anybody know a straight forward way of doing so for a gromacs trajectory? thank you very much, max -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
On 7/17/15 7:44 AM, Daniele Veclani wrote: OK! I got it. I have to put: couple-intramol = yes but I have to define couple-lambda 0 and couple-lamba-1? Yes, you have to tell mdrun what you're transforming. how do I turn off the 1-4 pair interaction? That requires explicit use of [pairs_nb], as I recall. There was a bug fix for that recently, so make sure you're using version 5.0.5. -Justin 2015-07-17 13:32 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 6:34 AM, Daniele Veclani wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. couple-intramol = no does not subject intramolecular interactions to lambda coupling. But doing this in vacuo is pointless, because then by definition, nothing changes. -Justin Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none
[gmx-users] CG: Tabulated potentials and temperature scaling
Dear Gromacs Users and Developers! I'm working on coarse graining of my molecules. I have obtained a set of coarse-grained potentials using IBI at one temperature. Now I would like to test temperature transferability - to check if my potentials will work at other temperatures. In order to run at new temperature, should I set the desired temperature in the mdp file only (keeping the tabulated potentials unchanged) or should I scale the tabulated potentials to the desired temperature? This question is actually the same as how gromacs works with the tabulated potentials - does it convert them from kJ/mol to kBT using the temperature from mdp file or not? Many thanks Anna -- Dr Anna Akinshina Research Fellow, University of Huddersfield Visiting Research Fellow, University of Manchester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] there are particles with all coordinates zero
On 7/17/15 12:21 AM, Carlos Navarro Retamal wrote: Dear gmx users, I was analysing some trajectories (without any problem), and then just for testing, i used gmx check on them, and i got several warnings: Reading frame3000 time 30.000 Warning at frame 3693: there are 1 particles with all coordinates zero Reading frame4000 time 40.000 Warning at frame 4052: there are 1 particles with all coordinates zero Warning at frame 4079: there are 1 particles with all coordinates zero Warning at frame 4271: there are 1 particles with all coordinates zero Warning at frame 4519: there are 1 particles with all coordinates zero Reading frame5000 time 50.000 Warning at frame 5063: there are 1 particles with all coordinates zero Reading frame6000 time 60.000 Warning at frame 6766: there are 1 particles with all coordinates zero Reading frame7000 time 70.000 Warning at frame 7403: there are 1 particles with all coordinates zero Warning at frame 7703: there are 1 particles with all coordinates zero Reading frame8000 time 80.000 Warning at frame 8667: there are 1 particles with all coordinates zero Warning at frame 8682: there are 1 particles with all coordinates zero Reading frame9000 time 90.000 Warning at frame 9752: there are 1 particles with all coordinates zero Last frame 1 time 100.000 Are this warnings that ‘bad'? Should i run again my simulations? Again, just seeing them by VMD, and by making some analysis on them with several gromacs tools(trjconv, msd, rdf, etc) i didn’t see any problem, or get any error/warning message, so i really don’t know what could be the problem (or if there is one, i don’t know how to fix it). Dump out one of those frames with trjconv and see if finding that particle is illustrative of anything. In reality, I doubt this is actually a problem because it just means that you (infrequently) have one particle exactly at the origin. -Justin Hope someone can help me, Best, Carlos ps- I tried to remove pbc conditions of the system, but i’m still getting the same error: -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
OK! I got it. I have to put: couple-intramol = yes but I have to define couple-lambda 0 and couple-lamba-1? how do I turn off the 1-4 pair interaction? 2015-07-17 13:32 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 6:34 AM, Daniele Veclani wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. couple-intramol = no does not subject intramolecular interactions to lambda coupling. But doing this in vacuo is pointless, because then by definition, nothing changes. -Justin Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds
Re: [gmx-users] Free Energy Calculations
On 7/17/15 3:35 AM, Live King wrote: Hi Everyone, I use ancient version of Gromacs 4.5.5 for free energy calculations. I have two different questions. 1) When I run g_bar for results, I get this lambda 0.000 - 0.050, DG -2.16 +/- 0.00 lambda 0.050 - 0.100, DG -2.16 +/- 0.01 lambda 0.100 - 0.150, DG -2.09 +/- 0.01 lambda 0.150 - 0.200, DG -1.98 +/- 0.01 lambda 0.200 - 0.250, DG -1.83 +/- 0.01 lambda 0.250 - 0.300, DG -1.59 +/- 0.00 lambda 0.300 - 0.350, DG -1.26 +/- 0.00 lambda 0.350 - 0.400, DG -0.80 +/- 0.00 lambda 0.400 - 0.450, DG -0.17 +/- 0.00 lambda 0.450 - 0.500, DG 0.67 +/- 0.00 lambda 0.500 - 0.550, DG 1.79 +/- 0.00 lambda 0.550 - 0.600, DG 3.30 +/- 0.01 lambda 0.600 - 0.650, DG 4.35 +/- 0.11 lambda 0.650 - 0.700, DG 1.99 +/- 0.10 lambda 0.700 - 0.750, DG 0.61 +/- 0.04 lambda 0.750 - 0.800, DG 0.04 +/- 0.02 lambda 0.800 - 0.850, DG -0.44 +/- 0.04 lambda 0.850 - 0.900, DG -0.46 +/- 0.02 lambda 0.900 - 0.950, DG -0.43 +/- 0.04 lambda 0.950 - 1.000, DG -0.49 +/- 0.02 total 0.000 - 1.000, DG -3.13 +/- 0.21 Where these results are stored. I don't seem to find them anywhere. Barint.xvg seems to contain something else. Please let me know if they get stored or not and If they don't please let me know how to store it ? ( of course without copy and pasting into the text file). g_bar -f *.xvg | tee bar.out 2) The results I showed above always show this warning :- *WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations.* I have checked for both possible suggestions.I don't seem to find anything wrong with my simulations. Sometimes this warning goes away if I increase the time span. But, most of the times it keeps coming back. What does that mean ? How can I get rid of that ? The warning is kind of cryptic, but in my experience indicates either insufficient sampling, inadequate topology, or wrong .mdp settings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
On 7/17/15 6:34 AM, Daniele Veclani wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. couple-intramol = no does not subject intramolecular interactions to lambda coupling. But doing this in vacuo is pointless, because then by definition, nothing changes. -Justin Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] problem in parametrization of NH2 group
On 7/17/15 2:31 AM, Nidhi Batra wrote: Dear All I want to run a simulation for a protein-peptide complex where the N- C-terminal of the peptide is capped by acetyl and amine (NH2) group respectively. I am using the charmm36ff but couldn't find the parameters for NH2 group anywhere. I tried using SwissParam to generate the .itp but don't know how to convert it to .rtp. Kindly help regarding this. From the CHARMM top_all36_prot.rtf: PRES CT2 0.00 ! amidated C-terminus GROUP ! use in generate statement ATOM CCC 0.55 ! ATOM OO -0.55 ! | GROUP ! O=C ATOM NT NH2-0.62 ! | ATOM HT1 H 0.32 ! NT ATOM HT2 H 0.30 !/ \ BOND C NT ! HT1 HT2 (HT1 is cis to O) BOND NT HT1 NT HT2 ! IMPR C NT CA O C CA NT O IMPR NT C HT1 HT2 NT C HT2 HT1 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. Can I do this? Best regards D.V. 2015-07-17 13:55 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 7:44 AM, Daniele Veclani wrote: OK! I got it. I have to put: couple-intramol = yes but I have to define couple-lambda 0 and couple-lamba-1? Yes, you have to tell mdrun what you're transforming. how do I turn off the 1-4 pair interaction? That requires explicit use of [pairs_nb], as I recall. There was a bug fix for that recently, so make sure you're using version 5.0.5. -Justin 2015-07-17 13:32 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 6:34 AM, Daniele Veclani wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. couple-intramol = no does not subject intramolecular interactions to lambda coupling. But doing this in vacuo is pointless, because then by definition, nothing changes. -Justin Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk : The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Re: [gmx-users] solvation free energy
I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe
Re: [gmx-users] solvation free energy
Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to center the molecule with trjconv
Hi Justin, Thanks for your comments, it's a big help. 2015-07-15 21:32 GMT+08:00 Justin Lemkul jalem...@vt.edu: On 7/14/15 11:20 PM, Zhenyu Meng wrote: Dear GROMACS users, I want to simulate DNA in a cubic box with water as solvent and visualize it. By using -pbc mol I can see part of the DNA is out of the box so I want to center the DNA in box. But using -center seems destruct the DNA into several parts. I tried to use -pbc mol followed by -center or -center followed by -pbc mol but both cannot center the DNA (the DNA doesn't fall apart but it's still not in the center). I'm curious about the algorithm about -center option. e.g. if I have a pbc cubic box with length of 5, and the COM of the DNA is at (3,3,3), in that way, if I use -center I think all the atoms of the system(including DNA and water) will shift with a vector(-0.5,-0.5,-0.5) to make sure the COM of DNA is now at(2.5,2.5,2.5) (the default boxcenter). Am I correct? Your help will be highly appreciated! For multi-chain molecules it is often helpful/necessary to center on one chain using an index group. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Sincerely, Mr. Meng Zhenyu Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Free Energy Calculations
Hi Everyone, I use ancient version of Gromacs 4.5.5 for free energy calculations. I have two different questions. 1) When I run g_bar for results, I get this lambda 0.000 - 0.050, DG -2.16 +/- 0.00 lambda 0.050 - 0.100, DG -2.16 +/- 0.01 lambda 0.100 - 0.150, DG -2.09 +/- 0.01 lambda 0.150 - 0.200, DG -1.98 +/- 0.01 lambda 0.200 - 0.250, DG -1.83 +/- 0.01 lambda 0.250 - 0.300, DG -1.59 +/- 0.00 lambda 0.300 - 0.350, DG -1.26 +/- 0.00 lambda 0.350 - 0.400, DG -0.80 +/- 0.00 lambda 0.400 - 0.450, DG -0.17 +/- 0.00 lambda 0.450 - 0.500, DG 0.67 +/- 0.00 lambda 0.500 - 0.550, DG 1.79 +/- 0.00 lambda 0.550 - 0.600, DG 3.30 +/- 0.01 lambda 0.600 - 0.650, DG 4.35 +/- 0.11 lambda 0.650 - 0.700, DG 1.99 +/- 0.10 lambda 0.700 - 0.750, DG 0.61 +/- 0.04 lambda 0.750 - 0.800, DG 0.04 +/- 0.02 lambda 0.800 - 0.850, DG -0.44 +/- 0.04 lambda 0.850 - 0.900, DG -0.46 +/- 0.02 lambda 0.900 - 0.950, DG -0.43 +/- 0.04 lambda 0.950 - 1.000, DG -0.49 +/- 0.02 total 0.000 - 1.000, DG -3.13 +/- 0.21 Where these results are stored. I don't seem to find them anywhere. Barint.xvg seems to contain something else. Please let me know if they get stored or not and If they don't please let me know how to store it ? ( of course without copy and pasting into the text file). 2) The results I showed above always show this warning :- *WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations.* I have checked for both possible suggestions.I don't seem to find anything wrong with my simulations. Sometimes this warning goes away if I increase the time span. But, most of the times it keeps coming back. What does that mean ? How can I get rid of that ? Thanks, Vikas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem in parametrization of NH2 group
Dear All I want to run a simulation for a protein-peptide complex where the N- C-terminal of the peptide is capped by acetyl and amine (NH2) group respectively. I am using the charmm36ff but couldn't find the parameters for NH2 group anywhere. I tried using SwissParam to generate the .itp but don't know how to convert it to .rtp. Kindly help regarding this. Thanking you Yours sincerely -- Nidhi Batra DBT-Research Associate Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar New Delhi 110020 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
On 7/17/15 12:06 PM, David van der Spoel wrote: On 17/07/15 17:55, Justin Lemkul wrote: On 7/17/15 11:29 AM, Daniele Veclani wrote: I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? If you need [ pairs_nb ], yes. But I actually don't think you do. See below. I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. I think you're reading this section backwards. Admittedly, it's a confusing section, so let's simplify. If you turn off the nonbonded interactions of some molecule in water, the total contribution to the free energy change is composed of the solute-solute terms and solute-water terms. To get the actual solvation free energy, one needs to correct for the solute-solute terms being turned off, which is the purpose of the gas-phase simulations. Turning off interactions in vacuo tells you how much of the free energy change is attributed to intramolecular terms. The difference between the two transformations is then the solvation free energy. But, several years ago, this procedure became much easier in GROMACS with the introduction of the couple-intramol keyword. It *eliminates* the need for any gas-phase simulations or topology hacking. This is what the manual is trying to tell you. If you run your transformations in water with couple-intramol = no, then the intramolecular interactions are always full strength, so the free energy difference you calculate is solely attributed to solute-water interactions, viz. the solvation free energy. If you *want* to make your life more difficult, set couple-intramol = yes and conduct gas-phase calculations, as well, which is what requires topology hacking. I wouldn't do this. Not only is the manual somewhat unclear, but any time you have to manually modify the topology, there is a potential for error. The free energy code attempts to make your life easy and efficient, unless you have some very complex protocol to do that requires lots of work. A solvation energy is not one of these cases; it is straightforward with appropriate use of the .mdp keywords. If I understand that correctly then the protocol ignores the difference in intramolecular energy between gas-phase and solvation. This is probably OK for small and rigid molecules but not necessarily for larger or flexible molecules. When using polarizable force fields it will probably induce a significant error. Have you tried this yet? We have not done a comparison. In CHARMM, we always explicitly do gas phase, but that is by necessity. We don't have an analogous couple-intramol-style behavior. It could probably be done, but we have an established protocol that has been used for years that is rock solid. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
On 7/17/15 11:29 AM, Daniele Veclani wrote: I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? If you need [ pairs_nb ], yes. But I actually don't think you do. See below. I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. I think you're reading this section backwards. Admittedly, it's a confusing section, so let's simplify. If you turn off the nonbonded interactions of some molecule in water, the total contribution to the free energy change is composed of the solute-solute terms and solute-water terms. To get the actual solvation free energy, one needs to correct for the solute-solute terms being turned off, which is the purpose of the gas-phase simulations. Turning off interactions in vacuo tells you how much of the free energy change is attributed to intramolecular terms. The difference between the two transformations is then the solvation free energy. But, several years ago, this procedure became much easier in GROMACS with the introduction of the couple-intramol keyword. It *eliminates* the need for any gas-phase simulations or topology hacking. This is what the manual is trying to tell you. If you run your transformations in water with couple-intramol = no, then the intramolecular interactions are always full strength, so the free energy difference you calculate is solely attributed to solute-water interactions, viz. the solvation free energy. If you *want* to make your life more difficult, set couple-intramol = yes and conduct gas-phase calculations, as well, which is what requires topology hacking. I wouldn't do this. Not only is the manual somewhat unclear, but any time you have to manually modify the topology, there is a potential for error. The free energy code attempts to make your life easy and efficient, unless you have some very complex protocol to do that requires lots of work. A solvation energy is not one of these cases; it is straightforward with appropriate use of the .mdp keywords. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella sampling - decomposing of free energy
Dear gromacs users, I did umbrella sampling in order to estimate the PMF profile of my system. My system has 512 water molecules covered by 25 decanol molecules on both side. I pulled a water molecule bulk water to organic layer and than gas phase. (Please see the system pic , http://imgur.com/sFFlVjF ) As a next step I wanted decompose this free energy in enthalpic and entropic contribution Delta G = Delta H - T Delta S Enthalpies ΔH were computed by averaging the potential energy over the respective simulation trajectory in each window (see the pic http://imgur.com/tc3cO95 ) My question is as you see there is big variation in enthalpy. What should I do to get more precise (less varied) potential energy? Simulation time 4 ns, time step is 2 fs, force field os GAFF (produced by topolbuild) As an example here one of the window potential energy http://imgur.com/Bw9aUpu Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling - decomposing of free energy
On 17/07/15 17:54, gozde ergin wrote: Dear gromacs users, I did umbrella sampling in order to estimate the PMF profile of my system. My system has 512 water molecules covered by 25 decanol molecules on both side. I pulled a water molecule bulk water to organic layer and than gas phase. (Please see the system pic , http://imgur.com/sFFlVjF ) As a next step I wanted decompose this free energy in enthalpic and entropic contribution Delta G = Delta H - T Delta S Enthalpies ΔH were computed by averaging the potential energy over the respective simulation trajectory in each window (see the pic http://imgur.com/tc3cO95 ) My question is as you see there is big variation in enthalpy. What should I do to get more precise (less varied) potential energy? Simulation time 4 ns, time step is 2 fs, force field os GAFF (produced by topolbuild) As an example here one of the window potential energy http://imgur.com/Bw9aUpu Thanks in advance Unfortunately the energy needs roughly ten times longer to equilibrate than the PMF! -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG: Tabulated potentials and temperature scaling
Dear Prof Chaban, Thank you very much for your fast reply! Best wishes Anna -- Dr Anna Akinshina Research Fellow, University of Huddersfield Visiting Research Fellow, University of Manchester -- On Fri, Jul 17, 2015 at 9:08 AM, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users and Developers! I'm working on coarse graining of my molecules. I have obtained a set of coarse-grained potentials using IBI at one temperature. Now I would like to test temperature transferability - to check if my potentials will work at other temperatures. In order to run at new temperature, should I set the desired temperature in the mdp file only (keeping the tabulated potentials unchanged) or should I scale the tabulated potentials to the desired temperature? Only in the MDP file. This question is actually the same as how gromacs works with the tabulated potentials - does it convert them from kJ/mol to kBT using the temperature from mdp file or not? I do not think the code uses kT as an internal unit in any procedure. Vitaly V. Chaban, Professor Many thanks Anna -- Dr Anna Akinshina Research Fellow, University of Huddersfield Visiting Research Fellow, University of Manchester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
On 17/07/15 17:55, Justin Lemkul wrote: On 7/17/15 11:29 AM, Daniele Veclani wrote: I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? If you need [ pairs_nb ], yes. But I actually don't think you do. See below. I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. I think you're reading this section backwards. Admittedly, it's a confusing section, so let's simplify. If you turn off the nonbonded interactions of some molecule in water, the total contribution to the free energy change is composed of the solute-solute terms and solute-water terms. To get the actual solvation free energy, one needs to correct for the solute-solute terms being turned off, which is the purpose of the gas-phase simulations. Turning off interactions in vacuo tells you how much of the free energy change is attributed to intramolecular terms. The difference between the two transformations is then the solvation free energy. But, several years ago, this procedure became much easier in GROMACS with the introduction of the couple-intramol keyword. It *eliminates* the need for any gas-phase simulations or topology hacking. This is what the manual is trying to tell you. If you run your transformations in water with couple-intramol = no, then the intramolecular interactions are always full strength, so the free energy difference you calculate is solely attributed to solute-water interactions, viz. the solvation free energy. If you *want* to make your life more difficult, set couple-intramol = yes and conduct gas-phase calculations, as well, which is what requires topology hacking. I wouldn't do this. Not only is the manual somewhat unclear, but any time you have to manually modify the topology, there is a potential for error. The free energy code attempts to make your life easy and efficient, unless you have some very complex protocol to do that requires lots of work. A solvation energy is not one of these cases; it is straightforward with appropriate use of the .mdp keywords. If I understand that correctly then the protocol ignores the difference in intramolecular energy between gas-phase and solvation. This is probably OK for small and rigid molecules but not necessarily for larger or flexible molecules. When using polarizable force fields it will probably induce a significant error. Have you tried this yet? -Justin -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling - decomposing of free energy
But why? On Fri, Jul 17, 2015 at 6:07 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 17/07/15 17:54, gozde ergin wrote: Dear gromacs users, I did umbrella sampling in order to estimate the PMF profile of my system. My system has 512 water molecules covered by 25 decanol molecules on both side. I pulled a water molecule bulk water to organic layer and than gas phase. (Please see the system pic , http://imgur.com/sFFlVjF ) As a next step I wanted decompose this free energy in enthalpic and entropic contribution Delta G = Delta H - T Delta S Enthalpies ΔH were computed by averaging the potential energy over the respective simulation trajectory in each window (see the pic http://imgur.com/tc3cO95 ) My question is as you see there is big variation in enthalpy. What should I do to get more precise (less varied) potential energy? Simulation time 4 ns, time step is 2 fs, force field os GAFF (produced by topolbuild) As an example here one of the window potential energy http://imgur.com/Bw9aUpu Thanks in advance Unfortunately the energy needs roughly ten times longer to equilibrate than the PMF! -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
Any particular reason why you want to do it the hard way? I suspect the answer to this is somewhere in section 5.3 where [pairs_nb] is discussed. You would have to explicitly set A and B states and not use couple-*. You may find some old-style input files on http://www.alchemistry.org/wiki/Main_Page . On Fri, 17 Jul 2015 12:34:42 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I read the manual and also some examples of free energy calculation. when I do the simulation: M(vacuo) -- nothing(vacuo) I leave only intramolecular interactions. How can I just leave these interactions? I don't find the answer in the manual. Best regards D.V. 2015-07-17 10:10 GMT+02:00 hannes.loeff...@stfc.ac.uk: I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the QUI label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state. I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI
Re: [gmx-users] Intel MKL taken in preference of the specified FFT library
Hi, That's a problem at your end, please search the mail archives. Mark On Fri, 17 Jul 2015 12:50 Reuti re...@staff.uni-marburg.de wrote: Hi Mark, thy for your reply and clarification about the library issue. Am 16.07.2015 um 20:43 schrieb Mark Abraham mark.j.abra...@gmail.com: Hi, On Thu, Jul 16, 2015 at 5:47 PM Reuti re...@staff.uni-marburg.de wrote: Hi, I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU compilers and a self compiled FFTW*. I configured Gromacs with: $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/home/reuti/local/fftw-3.3.4 As there was now shared version of FFTW it complains about it, and hence I compiled FFTW again - this time with shared library flag and the configure step of Gromacs succeeded. But after `make` and `make install` I faced the result, that the binary `gmx` like the library in lib64 were linked against Intel MKL. Well, there is an old version of the Intel MKL on the system and hence in the LD_LIBRARY_PATH. Once I cleared the LD_LIBRARY_PATH I got the result I expected. Older MKL had a feature of providing headers that look like FFTW but execute MKL, and programs will find that if it precedes real FFTW in the lookup path. Question: is this the intended behavior? IMO the GMX_FFT_LIBRARY=fftw3 flag should be honored first and any set LD_LIBRARY_PATH ignored. Yes, but Intel decided to be compatible a.k.a. deceptive. IIRC enough people complained that it got fixed for subsequent MKL. Meanwhile, our CMake code is quite complicated enough without double-checking for every possible rare case ;-) Meanwhile, there are ways of forcing the find mechanism to find the FFTW you really want. -- Reuti *) The automatic download (like outlined in the INSTALL: -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON) of FFTW and the regression tests points to the Gromacs site, but AFAICS they were moved to box.com, hence the automatic download fails. No, the FFTW download goes to its site, and the tests download goes to gerrit.gromacs.org. None of that has changed. For the FFTW you are right, I overlooked that it was complaining about the regression test only: * CMake Error at tests/CMakeLists.txt:57 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-5.1-rc1.tar.gz' failed status_code: 1 status_string: Unsupported protocol log: Hostname was NOT found in DNS cache Trying 130.237.25.133... Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-5.1-rc1.tar.gz HTTP/1.1 User-Agent: curl/7.38.0 Host: gerrit.gromacs.org Accept: */* HTTP/1.1 302 Found Date: Fri, 17 Jul 2015 10:08:02 GMT Server Apache/2.2.22 (Ubuntu) is not blacklisted Server: Apache/2.2.22 (Ubuntu) Location: https://kth.box.com/shared/static/xq0o95adj3076allx3feugtw4qrjlk9f.gz * Without the protocol error it would have downloaded from the final destination without getting noticed. But HTTP/1.1 302 Found is an URL redirect. -- Reuti Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] md-vv and md
Hi Michael, Has problem been solved about molecules drifting in md-vv integrator? Also can you please check my potential energy second pic in http://imgur.com/6aJkRoQfjXGmXu#0 . http://imgur.com/6aJkRoQfjXGmXu#0 What could be the reason this big jump in potential energy (integrator : md-vv)? And why I do not see the same jump by using md integrator? thanks in advance http://imgur.com/6aJkRoQfjXGmXu#0 On Mon, Jun 22, 2015 at 6:22 PM, gozde ergin gozdeeer...@gmail.com wrote: Hi Michael, There is one more question, I still could not get why do I see that big jump in potential energy? I understand all bulk is drifting in the box because of the COM removal step is omitted for md-vv but how this issue can effect the potential energy? best On Mon, Jun 22, 2015 at 4:05 PM, gozde ergin gozdeeer...@gmail.com wrote: Thanks Michael. On Mon, Jun 22, 2015 at 3:50 PM, Michael Shirts mrshi...@gmail.com wrote: At some point, a COM removal step was omitted for md-vv. A change has been proposed in in gerrit for a while (See https://gerrit.gromacs.org/#/c/4649/ and https://gerrit.gromacs.org/#/c/4467/ ), but one of the developers asked to have the source of the problem traced to understand better what happened and fixed at that point and merged forward. Hopefully this can get sorted out later this week. On Mon, Jun 22, 2015 at 9:10 AM, gozde ergin gozdeeer...@gmail.com wrote: Hi all, I was using md-vv as an integrator however I discovered that all bulk was moving (drifting) during the simulation. Than I changed the integrator and used md. The bulk molecules did not move during the simulation, just stayed in the middle of box. I attached the potential and kinetic energies of the systems with md-vv and md integrator. http://imgur.com/6aJkRoQfjXGmXu#0 When I use md-vv other than drifting, I also saw big jump in potential energy after 10ns. However this is not the case for md integrator system. Is this normal? Does anyone face with the same problem? What could be the reason for that? thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
On 7/17/15 12:08 PM, Justin Lemkul wrote: On 7/17/15 12:06 PM, David van der Spoel wrote: On 17/07/15 17:55, Justin Lemkul wrote: On 7/17/15 11:29 AM, Daniele Veclani wrote: I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? If you need [ pairs_nb ], yes. But I actually don't think you do. See below. I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. I think you're reading this section backwards. Admittedly, it's a confusing section, so let's simplify. If you turn off the nonbonded interactions of some molecule in water, the total contribution to the free energy change is composed of the solute-solute terms and solute-water terms. To get the actual solvation free energy, one needs to correct for the solute-solute terms being turned off, which is the purpose of the gas-phase simulations. Turning off interactions in vacuo tells you how much of the free energy change is attributed to intramolecular terms. The difference between the two transformations is then the solvation free energy. But, several years ago, this procedure became much easier in GROMACS with the introduction of the couple-intramol keyword. It *eliminates* the need for any gas-phase simulations or topology hacking. This is what the manual is trying to tell you. If you run your transformations in water with couple-intramol = no, then the intramolecular interactions are always full strength, so the free energy difference you calculate is solely attributed to solute-water interactions, viz. the solvation free energy. If you *want* to make your life more difficult, set couple-intramol = yes and conduct gas-phase calculations, as well, which is what requires topology hacking. I wouldn't do this. Not only is the manual somewhat unclear, but any time you have to manually modify the topology, there is a potential for error. The free energy code attempts to make your life easy and efficient, unless you have some very complex protocol to do that requires lots of work. A solvation energy is not one of these cases; it is straightforward with appropriate use of the .mdp keywords. If I understand that correctly then the protocol ignores the difference in intramolecular energy between gas-phase and solvation. This is probably OK for small and rigid molecules but not necessarily for larger or flexible molecules. When using polarizable force fields it will probably induce a significant error. Have you tried this yet? We have not done a comparison. In CHARMM, we always explicitly do gas phase, but that is by necessity. We don't have an analogous couple-intramol-style behavior. It could probably be done, but we have an established protocol that has been used for years that is rock solid. I would also agree that there would be massive errors for a polarizable force field in this case due to environmental response. I assume, for now, most people are using additive models. In fact, until I have actually tested the free energy code with our Drude model, it is explicitly disabled by grompp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] solvation free energy
Then as I had already calculated the free energy in a box with solute and solvent with the option couple-intramol = no, I already have the solvatation free energy correct, Is it right?? D.V. 2015-07-17 18:10 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/17/15 12:08 PM, Justin Lemkul wrote: On 7/17/15 12:06 PM, David van der Spoel wrote: On 17/07/15 17:55, Justin Lemkul wrote: On 7/17/15 11:29 AM, Daniele Veclani wrote: I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ? If you need [ pairs_nb ], yes. But I actually don't think you do. See below. I read in the manual (section 5.3.4) that can turn off the 1-4 interactions without ever touching the topology, by using the couple-moltype, couple-lambda0, couple-lambda 1, and couple-intramol keywords. I think you're reading this section backwards. Admittedly, it's a confusing section, so let's simplify. If you turn off the nonbonded interactions of some molecule in water, the total contribution to the free energy change is composed of the solute-solute terms and solute-water terms. To get the actual solvation free energy, one needs to correct for the solute-solute terms being turned off, which is the purpose of the gas-phase simulations. Turning off interactions in vacuo tells you how much of the free energy change is attributed to intramolecular terms. The difference between the two transformations is then the solvation free energy. But, several years ago, this procedure became much easier in GROMACS with the introduction of the couple-intramol keyword. It *eliminates* the need for any gas-phase simulations or topology hacking. This is what the manual is trying to tell you. If you run your transformations in water with couple-intramol = no, then the intramolecular interactions are always full strength, so the free energy difference you calculate is solely attributed to solute-water interactions, viz. the solvation free energy. If you *want* to make your life more difficult, set couple-intramol = yes and conduct gas-phase calculations, as well, which is what requires topology hacking. I wouldn't do this. Not only is the manual somewhat unclear, but any time you have to manually modify the topology, there is a potential for error. The free energy code attempts to make your life easy and efficient, unless you have some very complex protocol to do that requires lots of work. A solvation energy is not one of these cases; it is straightforward with appropriate use of the .mdp keywords. If I understand that correctly then the protocol ignores the difference in intramolecular energy between gas-phase and solvation. This is probably OK for small and rigid molecules but not necessarily for larger or flexible molecules. When using polarizable force fields it will probably induce a significant error. Have you tried this yet? We have not done a comparison. In CHARMM, we always explicitly do gas phase, but that is by necessity. We don't have an analogous couple-intramol-style behavior. It could probably be done, but we have an established protocol that has been used for years that is rock solid. I would also agree that there would be massive errors for a polarizable force field in this case due to environmental response. I assume, for now, most people are using additive models. In fact, until I have actually tested the free energy code with our Drude model, it is explicitly disabled by grompp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] md-vv and md
Has problem been solved about molecules drifting in md-vv integrator? We think so, but some additional tests are running to address any other lingering integrator issues. The fix is in 5.1 beta, but not in the 4.6 branch yet (it's a pull request, but not yet merged). Also can you please check my potential energy second pic in http://imgur.com/6aJkRoQfjXGmXu#0 . http://imgur.com/6aJkRoQfjXGmXu#0 What could be the reason this big jump in potential energy (integrator : md-vv)? And why I do not see the same jump by using md integrator? I don't think there's sufficient information here to answer that question. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cross-correlation map of protein residues
There is a modified version of g_covar available at the below link for calculating correlation matrix: http://www.gromacs.org/Downloads/User_contributions/Other_software http://www.gromacs.org/@api/deki/files/55/=g_covar.tgz -- Thanks and Regards, Bipin Singh On Fri, Jul 17, 2015 at 6:51 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: Dear list, I am looking for a gromacs tool which is able to calculate/draw a map of residues which are either in their motion correlated or anti correlated. first i thought i could just use g_covar with c-alpha and use the -xpma option but while reading previous mailing list posts people said that the atomic covariance matrix does not correlate motions. All posts I found where older and the script from the gromacs site for a g_covar tool which can calculate the correlation plot is from 2009. Therefore, i wanted to know if gromacs 5 is able to directly calculate the plot. if not does anybody know a straight forward way of doing so for a gromacs trajectory? thank you very much, max -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to extract energies from the Gromacs trajectory file
I am facing problem in extracting energies from the gromacs trajectory file (traj.xtc).and how to extract configuration from it? Rabindra Raj Oliya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS 5.0.5 GPU version on K620
Krzysztof, Whyle GROMACS 5.0.x build system does not explicitly generate options targeting 5.x devices, the binary built should still be compatible with your GPU. You can try adding the device-specific optimization flags with the -DCUDA_NVCC_FLAGS_RELEASE=-gencode;arch=compute_50,code=sm_50 cmake flag, but I'm not sure this fix the issue. What does gmx -version show? Cheers, -- Szilárd On Fri, Jul 17, 2015 at 11:49 PM, Krzysztof Kuczera kkucz...@ku.edu wrote: Hi Group, I am getting a run-time error on my Linux workstation with K620 GPU for the GPU version of GROMACS 5.0.5 using gcc 4.8.3 and CUDA Toolkit 7.0 I had no problem compiling the code but got this error when starting a test case: Program mdrun, VERSION 5.0.5 Source code file: /home/kuczera/prog/gromacs-5.0.5/src/gromacs/mdlib/nbnxn_cuda/ nbnxn_cuda.cu, line: 619 Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb: an illegal memory access was encountered Searching the Web, I found that this type of error was already resolved in GROMACS 4.6 some time ago. Could somebody suggest a solution? We have been able to compile and run GROMACS 5.0.4 on an older GPU with compute capability 3.5, my newer K620 has compute capability 5.0 - could this be the problem ? Thanks Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 1251 Wescoe Hall Drive, 5090 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cross-correlation Dihedral Angle
Hi All, I have a 1 microsecond trajectory of a 11-residue peptide sequence. I want to identify how the movement/change of one dihedral angle dictates the dynamics of the other ones (if any). I was wondering if there is a way to estimate cross-correlation matrix (something similar to what can be obtained by using g_covar for C-alpha atoms) for dihedral angles. ThanksAtanu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROMACS 5.0.5 GPU version on K620
Hi Group, I am getting a run-time error on my Linux workstation with K620 GPU for the GPU version of GROMACS 5.0.5 using gcc 4.8.3 and CUDA Toolkit 7.0 I had no problem compiling the code but got this error when starting a test case: Program mdrun, VERSION 5.0.5 Source code file: /home/kuczera/prog/gromacs-5.0.5/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu, line: 619 Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb: an illegal memory access was encountered Searching the Web, I found that this type of error was already resolved in GROMACS 4.6 some time ago. Could somebody suggest a solution? We have been able to compile and run GROMACS 5.0.4 on an older GPU with compute capability 3.5, my newer K620 has compute capability 5.0 - could this be the problem ? Thanks Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 1251 Wescoe Hall Drive, 5090 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
