Re: [gmx-users] Charmm Sugars/carbohydrates
All of the Charmm force field parameters may be found on Alex MacKerell's website: http://mackerell.umaryland.edu/ CHARMM_ff_params.html. Converting from Charmm units and potential form to Gromacs is straightforward. Andrew On Dec 7, 2011, at 12:59 PM, Michael McGovern wrote: Hi everyone. I'm doing a simulation in gromacs using the charmm36 parameters from the gromacs website. The parameters don't seem to have carbohydrates, which are part of the charmm36 force field. In particular, I need parameters for trehalose. Is there anywhere I can find these parameters in a format suitable for gromacs? -- 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] Non zero total charge
I believe your problem is that you do not understand scientific notation. 5.70e+01 = 57. Cl- has a charge of -1. Need I say more. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia munishikaka...@yahoo.comwrote: Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error: System has non-zero total charge: 5.70e+01 So i should add another 5 CL ions to neutralize the system? Many thanks, Munishika -- 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] Lennard Jones interactions
You can calculate that by hand on a calculator in a few seconds. There is no need to use Gromacs. On Jun 10, 2011, at 2:27 PM, Nilesh Dhumal wrote: Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] Lennard Jones interactions
The LJ interaction is 0. But you're asking about a bond. 1-2 interactions are typically modeled with a harmonic potential. This is most definitely not zero. On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote: If eplilon of hydrogen atom is zero then the lennard jones interaction of OH bond (at 0.22nm)is also zero. Is it correct? I used equation 4.5 to calculate LJ energy. Nilesh On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? Using energygrps might be an option if you need to monitor the interaction over time. Otherwise, if the distance is fixed, just plug all the parameters into the LJ equation. In theory, you could calculate the interactions this way over time, as well, even if the distance changes. -Justin I am using Gromacs 4.0.7 version. Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] OPLS and RB parameters in GROMACS
There is no error. The alkane dihedral parameters were updated in 1999, and differ from those originally published in 1996. Andrew On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mssula...@gmail.com wrote: Hi all, Hi I've converted the OPLS-AA torsional potential parameters for the alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found that the calculated values are different. A previous post to the gmx-users mailing list on March 27, 2008, pointed out this issue for the H-C-C-H torsional potential but there was no response to that. Does anyone know if there is an error in the ffoplsaabon.itp file? Or is there a newer set of OPLS-AA parameters? For the OPLS-AA parameters (in kcal/mol), I used: dihedral V1 V2 V3 C-C-C-C1.740 -0.157 0.279 C-C-C-H 0.0 0.00.366 H-C-C-H 0.0 0.00.318 from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: dihedral C0 C1 C2 C3 C-C-C-C3.56686 -1.889076 0.65688 -2.33467 C-C-C-H 0.66526 1.99577 0.0 -2.661024 H-C-C-H 0.76567 -2.297020.0 -3.06269 the parameters in the ffoplsaabon.itp file are: dihedral C0 C1 C2 C3 C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 C-C-C-H 0.6276 1.882800.0 -2.5104 H-C-C-H 0.6276 1.8828 0.0 -2.5104 Thankyou for any clarification. Sulatha -- 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] TIP3P water box
If you get this to work, you may still have problems as SPC and TIP3P have different geometries. A box of 216 waters is pretty easy to equilibrate; you could have this done for TIP3P in no time at all. On Apr 16, 2010, at 4:46 AM, kecy...@sina.com wrote: Hello,I want to use spc216.gro and apply the tip3p.itp parameters, but it would make a mistake for the pre-processor grompp ,it said can't find HW atomtypes, the force file which I used is ffG43a1.itp. my tip3p.itp file is as follows: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 10.417 3 opls_112 1 SOL HW2 10.417 #endif #ifdef _FF_CHARMM 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 #endif #ifdef _FF_GROMACS 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #endif #ifdef _FF_GROMOS96 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572 502416.0 1 3 1 0.09572 502416.0 0.09572 502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif the version of the gromacs is 4.0.5. Thank you for all 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with calculating Cv and Cp
Lum, You'll have better luck if you perform a few simulations at different temperatures at the same pressure and mole number, and then numerically differentiate the resulting enthalpy. I believe that the default heat capacity that Gromacs will print out is only valid for NVE simulations, and I am not sure of the formulas that you are referring to from Allen and Tildesley J.M. Haile. Also, don't expect your calculated heat capacity with TIP3P to agree the experimental value. You should under-predict the experimental value. Lastly, depending on what you are interested in, you may have better luck with a water model other than TIP3P. Hope this helps, Andrew ___ ___ Andrew Paluch Department of Chemical and Biomolecular Engineering University of Notre Dame du Lac apal...@nd.edu ___ ___ On Dec 9, 2009, at 8:18 PM, Lum Nforbi wrote: Dear all, I have run an 8 ns NPT simulation of 2000 molecules of TIP3P water and I have a very low Cv value of 12.4748 J/mol K (factor = 0.000164481). The result is below. I ignored this value and have tried using formulas for Cv that I found in the two books: Allen and Tildesley J. M. Haile but I can't come out with the right answer. Has anyone ever calculated Cv or Cp for water manually from scratch and gotten the right answer? If so, please, could you give me the details of what you did? Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift -- - Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.0001642811.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_current
Does anyone know of a reference (besides the manual) for the calculations performed by g_current? Thank you, Andrew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 1-4 interactions
You can either specify this explicitly or use the fudge LJ and fudge q headers in your topology file. See the manual for details. On Sep 26, 2009, at 1:51 AM, Vitaly V. Chaban wrote: Hi, Is it possible in gromacs to make 1-4 interaction energy reduced as compared to the intermolecular interations between the same centers? In other words, I want the INTRAmolecular interaction A-B to be by some factor smaller than INTERmolecular A-B interactions in the box. Thanks, Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Buckingham Potential
To whom this may concern, I am performing simulations for a system that is modeled with a Buckingham potential and PME for the electrostatic interactions. I have developed my forcefield file such that non-bonded cross terms are listed in a table, and also 1-4 interactions are listed in a table with an LJ type of potential. On 16 processors, I am able to run my system for 0.5ns in a day. If I map the potential to an LJ, I am able to achieve 2.5ns in a day. Does anyone have any idea as to where my performance loss may be occurring? Are there any special compilation or run-time flags that I should be using? Thank you, Andrew ___ ___ Andrew Paluch Department of Chemical and Biomolecular Engineering University of Notre Dame du Lac apal...@nd.edu ___ ___ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FudgeLJ
To whom this may concern, Is it possible to use FudgeLJ to scale 1-4 interactions when using a Buckingham Potential? Also, are long range corrections implemented for the Buckingham Potential? Thank you, Andrew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
