[gmx-users] Energy Calculation
Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? -- 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] value of an angle
Hi, if you are interested in a particular angle (between a triad of atoms) you can specify it in angle.ndx file (to generate the angles run: mk_angndx -s topol.tpr -n angle.ndx) the -ov flag of g_angle will generate the angle trajectory and the -od flag will generate its distribution cheers On Wed, Feb 24, 2010 at 10:22 PM, Carla Jamous carlajam...@gmail.comwrote: Hi everyone, please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average. Thanks, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Energy Calculation
simon sangma wrote: Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? g_energy -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] System has non-zero total charge: -8.000001e+00
Maurício Menegatti Rigo wrote: IS this a problem? /System has non-zero total charge: -8.01e+00/ If yes, can I fix that changing COulomb cutt-off to PME electrostatics? You need to add counterions to your system. Consult some basic tutorial material, as well as the manual entry for genion. -Justin THanks!! -- 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/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] Steered Molecular Dynamics (SMD)
Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I expected. Part of my .gro file and .mdp file are below. By using them, the COM of the slab of griphene moved at a constant speed, but the 'slab' crashed. Because not all the carbon atoms moved at the same speed. In order to produce the results that I want, which pull type (no, umbrella, constraint or constant_force) and which pull geometry (distance, direction, cylinder or position) shall I use? There is no reference group in my simulation. Do I need to modify the .gro file? Part of the .gro file: ... 4917sla C11093 1.265 1.609 0.237 4918sla C11094 1.549 1.609 0.237 4919sla C11095 1.336 1.486 0.237 4920sla C11096 1.478 1.486 0.237 4921sla C11097 1.691 1.363 0.237 4922sla C11098 1.975 1.363 0.237 4923sla C11099 1.762 1.240 0.237 4924sla C11100 1.904 1.240 0.237 4925sla C11101 2.117 1.363 0.237 4926sla C11102 2.401 1.363 0.237 ... These are all the carbon atoms of the slab of griphene. The Pulling Code: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= direction ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 10 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = pull_weights0= pull_pbcatom0= 0 pull_group1 = sla pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 0.237 pull_rate1 = 5e-4 pull_k1 = pull_kB1 = Any suggestions are welcome! Thank you in advance!-- 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] System has non-zero total charge: -8.000001e+00
You should always neutralise your sysem. On Thu, Feb 25, 2010 at 1:42 PM, Maurício Menegatti Rigo mauriciomr1...@gmail.com wrote: IS this a problem? *System has non-zero total charge: -8.01e+00* If yes, can I fix that changing COulomb cutt-off to PME electrostatics? THanks!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] energy minimization problem
Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able to get the Fmax below e-02. i have tried using the l-bgs minimization technique. The lbfgs.mdp file is as follows define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit= 0 nsteps = 1 nbfgscorr= 10 emtol= .001 emstep = 0.5 gen_vel = no gen-temp = 300 nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.2 rvdw = 1.0 Tcoupl = no Pcoupl = no coulombtype = PME vdwtype = shift The minimization continues up to the specified no. of steps. When I try to give another minimization run on the minimized structure, the Fmax goes upto the order e+00. I am not being able to figure out the problem. Any suggestion regarding this will be very helpful. Thanks in advance Sarbani. -- 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] Order parameter for unsaturated lipid chain in UA model
Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. Thank you, Sarah -- 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] Order parameter for unsaturated lipid chain in UA model
Sarah Witzke wrote: Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. I don't see why a drop in the order parameter is unexpected. I see it all the time in published papers of unsaturated lipids, for example: http://pubs.acs.org/doi/abs/10.1021/jp902131b http://www3.interscience.wiley.com/journal/114209721/abstract -Justin Thank you, Sarah -- 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/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
SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Thank you for your quick respons! It is not so much the drop, but more the position and the prescens of a small drop, then a little rise and then the big drop. I have pasted the file in below. Do you think my method of replacing the order parameters for the double bonded atoms is ok? Order parameters sn-2 chain POPC* 1 0.176177 20.18184 3 0.182874 4 0.180724 5 0.167932 6 0.162731 7 0.107512 8 0.139351 9 0.0311607 10 0.0519802 11 0.095191 12 0.0884555 13 0.0930531 14 0.0787042 15 0.0732823 16 0.0541174 ** Thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: to 25-02-2010 14:42 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel Sarah Witzke wrote: Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. I don't see why a drop in the order parameter is unexpected. I see it all the time in published papers of unsaturated lipids, for example: http://pubs.acs.org/doi/abs/10.1021/jp902131b http://www3.interscience.wiley.com/journal/114209721/abstract -Justin Thank you, Sarah -- 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/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] value of an angle
Thank you for your replies, indeed it worked! But now, I'm looking for a command line that allows me to calclulate the RMSF (or if you prefer, the distance between Calpha) between 2 static structures. Carla On Thu, Feb 25, 2010 at 11:55 AM, Amir Marcovitz amarcov...@gmail.comwrote: Hi, if you are interested in a particular angle (between a triad of atoms) you can specify it in angle.ndx file (to generate the angles run: mk_angndx -s topol.tpr -n angle.ndx) the -ov flag of g_angle will generate the angle trajectory and the -od flag will generate its distribution cheers On Wed, Feb 24, 2010 at 10:22 PM, Carla Jamous carlajam...@gmail.comwrote: Hi everyone, please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average. Thanks, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 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] value of an angle
On 26/02/2010 1:11 AM, Carla Jamous wrote: Thank you for your replies, indeed it worked! But now, I'm looking for a command line that allows me to calclulate the RMSF (or if you prefer, the distance between Calpha) between 2 static structures. Look in section 7.4 of the manual for a run-down on the utility programs. Then use the -h flag on likely-looking ones. If you learn to find out how to solve your own problems, you can produce results faster than if you wait 24 hours for an email :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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: SV: SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah Witzke wrote: Thank you for looking at the data. I just thought, that it deviated too much from published results, but perhaps it is because I have mainly worked with saturated lipids. I calculated the order over the last 117 ns of a 167 ns trajectory (10 ps between each frames), so there should be sufficient data I think. Thank you, Sarah Did you look at the papers I linked earlier? Your results look pretty similar to the data from those papers, which included both experimental and computational information. If you're not used to unsaturated lipids, have a look around the literature - there's lots out there! -Justin Fra: Justin A. Lemkul [mailto:jalem...@vt.edu] Sendt: to 25-02-2010 15:14 Til: Sarah Witzke Emne: Re: SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel Sarah Witzke wrote: Thank you for your quick respons! It is not so much the drop, but more the position and the prescens of a small drop, then a little rise and then the big drop. I have pasted the file in below. Do you think my method of replacing the order parameters for the double bonded atoms is ok? This all looks pretty normal to me, perhaps a little rocky from insufficient sampling? Usually the curves are a bit smoother, but the plot of these data look very much like the published results for other unsaturated lipids. -Justin Order parameters sn-2 chain POPC* 1 0.176177 20.18184 3 0.182874 4 0.180724 5 0.167932 6 0.162731 7 0.107512 8 0.139351 9 0.0311607 10 0.0519802 11 0.095191 12 0.0884555 13 0.0930531 14 0.0787042 15 0.0732823 16 0.0541174 ** Thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: to 25-02-2010 14:42 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel Sarah Witzke wrote: Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. I don't see why a drop in the order parameter is unexpected. I see it all the time in published papers of unsaturated lipids, for example: http://pubs.acs.org/doi/abs/10.1021/jp902131b http://www3.interscience.wiley.com/journal/114209721/abstract -Justin Thank you, Sarah -- 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 list gmx-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 -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
[gmx-users] problem with freezing group size
Dear all, I am sorry for poorly describing my problem about the freezing group size. Here I am giving my question very briefly, can anybody help me please? I would like to know the relation between the size of freezing group and the temperature coupling. when I separate the temperature coupling for freezing and non freezing groups the initial temperature for whole system is showing me zero in the log file, and the non-freezing group is just vibrating not at all moving during the course of simulation. This is true only when I am using large freezing group (freezing group has 26540 atoms and non-freezing group has around 9000 atoms). However if I use small freezing group (freezing group has 7340 atoms and non-freezing group has around 25840 atoms) I am getting log file with initial temperature as 300K, and the non-freezing group is moving well and the diffusion coefficient of solvent is matching with its corresponding value in the bulk (with out freezing). I hope somebody understand my problem now!!! thanks very much. Thanks in advance Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] energy minimization problem
Actual text input / output would be a good idea here. What is the actual output when you try to run it the second time? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of sarbani chattopadhyay Sent: Friday, 26 February 2010 12:06 AM To: gmx-users@gromacs.org Subject: [gmx-users] energy minimization problem Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able to get the Fmax below e-02. i have tried using the l-bgs minimization technique. The lbfgs.mdp file is as follows define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit = 0 nsteps = 1 nbfgscorr = 10 emtol = .001 emstep = 0.5 gen_vel = no gen-temp = 300 nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.0 Tcoupl = no Pcoupl = no coulombtype = PME vdwtype = shift The minimization continues up to the specified no. of steps. When I try to give another minimization run on the minimized structure, the Fmax goes upto the order e+00. I am not being able to figure out the problem. Any suggestion regarding this will be very helpful. Thanks in advance Sarbani. http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle? ~WRD000.jpg-- 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] query about free energy landscape
Dear Sir, I am facing one problem regarding generation of Free energy landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be highly obliged if you kindly let me clear my doubt. I know that three variables are needed for construction of 3D energy landscape. The free energy = -KBTln(probability of conformational distribution). But I can not understand how to find the conformational distribution, is it already embedded in the algorithm of g_sham? I followed the following procedure mentioned below. First I prepared an xvg file with 3 columns; the first is the time frame, 2nd and 3rd parameters are the parameters I want to calculate, for eg the projections along 1st and 2nd Principal Components. Then I used the command g_sham –f *.xvg -ls Then I converted gibbs.xpm into an eps file using xpm2ps –rainbow. The file that I obtained is not showing free energy landscape, rather an eps file is generated which contains some scattered square like conformations. Please suggest If I am doing anything wrong. Should I follow the same procedure while generating the FEL using other variables like potential energy, Rg or RMSD? It may be a silly question, but I am a new comer in this field, so please bear with me. Your urgent help in this matter is highly appreciated. Regards Sangeeta The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
