Re: [gmx-users] About Pulling code in Gromacs 5.0.2
The artifacts warning is general (mentioned in the manual) and has nothing to do with your system (aside from your mdp), everyone using absolute reference frame gets this warning. That said, the error you're getting is actually descriptive. So: 1. Check if the system is stable and happy without pulling. 2. Make sure the pulling rate is compatible with your nstlist setting. If the neighbor list update rate can't keep up with your pulling rate, that's a problem. High pulling rates in thermostatted systems are also generally problematic from the physical standpoint. Severely problematic. Steered MD is to be carefully designed. 3. Make sure your boundaries are taken care of properly, in case your pulled object meets the wall. Alex hy Hello all, hy Recently, I preformed a SMD, pulling a nano diamond across the membrane. I hy found that pull_geometry position in the Gromacs 4.6.5 (suggested in the hy tips of the US tutorial by Justin.A ) was replaced by pulling with absolute hy reference point in Gromacs 5.0.2. After defined pulling parameters hy according to the manual, Gromacs gave me a warning that This will lead to hy artifacts. I really want to know what did it mean, so I ignored it by hy using maxwarn 1 and saw what would happen. Finally I got a segment fault hy that a bonded atom moved away, out of the cut-off distance. hy Can you give me some advises? How can I treat the pulling correctly for hy this penetrating process and why does the absolute reference lead to hy artifacts. hy Many thanks! hy Hang -- 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] Different Cv and Cp
Dear Michael, Could you please comment on my last question, thanks a lot. I have noticed that when I run both NVT and NPT simulations from a same .gro file (obtained from energy minimization) I obtain same Cv and Cp for two ensembles. However, so far I was running NVT after NPT (meaning I used .gro file obtained from NPT as initial configuration for NVT, since I wanted to have correct volume). The second way gives that big difference in Cv and Cp. I run a long simulations in all cases, but why both ways produce such difference? Best regards On Tue, Jun 9, 2015 at 5:45 PM, Michael Shirts mrshi...@gmail.com wrote: The variance formula is derived from the derivative formula + the assumption the distribution in Boltzmann, so they must agree if the distribution is Boltzmann. On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Thank you so much for the reply. Yes, I use contact applied pressure and I am careful about units. I checked and average enthalpy and U are close, meaning that PV is negligible. But the point is variance of enthalpy in NPT differs from variance of energy in NVT and that causes the difference. You had given me an article showing that for example for Benzene the difference in Cv and Cp is 25%, and here Ii get similar ( my molecule is also carbon ring). But still I can answer why two both ways does not give same Cv-Cp. I will follow your suggestion. Best regards On Tue, Jun 9, 2015 at 5:29 PM, Michael Shirts mrshi...@gmail.com wrote: If the simulation are generating configurations with the Boltzmann probability distribution, the results should the same up to error. Cv and Cp should not be exactly the same, though for liquids at room temperature, they are pretty close (look up the precise numbers for the fluid you are interested in). Are you calculating enthalpy as U + PV, where P is the constant APPLIED pressure, not the instantaneous pressure, and PV is in same units? Since the PV term should be quite low for liquids, the two heat capacities should be relatively close (within noise -- fluctuation based calculations I think are noisier). Else you need to check if the Boltzmann distributions are being correctly generated: See the code and paper describing it linked here: https://github.com/shirtsgroup/checkensemble On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Can I ask a question concerning your previous email, I followed Cv = (dU/dT)_V Cp = (dH/dT)_P for my lutidine molecule, and I get same values for Cv and Cp. But when I test with kB T^2 c_P = Var (Enthalpy) kB T^2 c_V = Var (Energy) I get 40 J/mol.K difference in Cv and Cp. Mean that fluctuation play big role. Which way of checking I can rely? Best regards On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com wrote: By definition (more fundamental that fluctuation formulas) Cv = (dU/dT)_V Cp = (dH/dT)_P Run two simulations at different T and estimate the derivatives. On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, I still would like to know what was your method you mentioned on last paragraph, just for learning: ''Also, to be sure, you should double check by calculating both heat capacities by finite difference formulas as well with two simulations at T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls don't agree within propagated error, then something is off.'' ? thanks Best regards On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Andre, thank you for the link, you are probably right, It seems that my molecule has the difference Cp-Cv in the same range as benzene (since it has also ring structure). Best regards On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, I use Parrinello-Rahman for barostat and v-rescale for thermostat. Sorry, could you explain more the second paragraph please? I did not get the method. What I checked so far is checking if gromacs correctly gives Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives. Best regards On Mon, May 25, 2015 at 4:11 PM, Michael Shirts mrshi...@gmail.com wrote: Are you running with the Berendsen thermostat or barostat? The gromacs g_energy functions for heat capacity
Re: [gmx-users] g_wham error in umbrella simulation
Hi，高 发银行卡号给我，我还你钱，你结婚肯定要用钱吧 Sent from my Huawei Mobile Ming Tang m21.t...@qut.edu.au wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks -- 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] GPU acceleration
PS: if you are very concerned about cooling why not look at some gaming benchmarks of GTX 960 boards by different manufacturers and pick the one with the best cooling, e.g. here's one such review: http://www.tomshardware.com/reviews/evga-super-super-clocked-gtx-960,4063-4.html -- Szilárd On Wed, Jun 10, 2015 at 4:00 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Jun 10, 2015 at 4:21 AM, Alex nedoma...@gmail.com wrote: At this point, we will be getting the card for sure, likely the GTX 960 you suggested. Hence, a question. Which of the manufacturers would you recommend in terms of cooling (if you think it might become an issue with week or so long runs)? I can't really give you much recommendation in terms of manufacturer. I typically suggest people to stay away from factory overclocked cards (although some have been reporting stable use for years of such cards). Otherwise the GTX 960 is not a beast in terms of power consumption and I would not expect cooling to be much of an issue. I doubt we'll be needing the 4GB version, so my only concern is cooling. Comments highly appreciated. Thanks, Alex -- 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] Different Cv and Cp
I can't diagnose what is wrong in every case; I can just say that statistical mechanics says that both methods for calculating Cv and both methods for calculating Cp should agree within noise. On Wed, Jun 10, 2015 at 8:54 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Could you please comment on my last question, thanks a lot. I have noticed that when I run both NVT and NPT simulations from a same .gro file (obtained from energy minimization) I obtain same Cv and Cp for two ensembles. However, so far I was running NVT after NPT (meaning I used .gro file obtained from NPT as initial configuration for NVT, since I wanted to have correct volume). The second way gives that big difference in Cv and Cp. I run a long simulations in all cases, but why both ways produce such difference? Best regards On Tue, Jun 9, 2015 at 5:45 PM, Michael Shirts mrshi...@gmail.com wrote: The variance formula is derived from the derivative formula + the assumption the distribution in Boltzmann, so they must agree if the distribution is Boltzmann. On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Thank you so much for the reply. Yes, I use contact applied pressure and I am careful about units. I checked and average enthalpy and U are close, meaning that PV is negligible. But the point is variance of enthalpy in NPT differs from variance of energy in NVT and that causes the difference. You had given me an article showing that for example for Benzene the difference in Cv and Cp is 25%, and here Ii get similar ( my molecule is also carbon ring). But still I can answer why two both ways does not give same Cv-Cp. I will follow your suggestion. Best regards On Tue, Jun 9, 2015 at 5:29 PM, Michael Shirts mrshi...@gmail.com wrote: If the simulation are generating configurations with the Boltzmann probability distribution, the results should the same up to error. Cv and Cp should not be exactly the same, though for liquids at room temperature, they are pretty close (look up the precise numbers for the fluid you are interested in). Are you calculating enthalpy as U + PV, where P is the constant APPLIED pressure, not the instantaneous pressure, and PV is in same units? Since the PV term should be quite low for liquids, the two heat capacities should be relatively close (within noise -- fluctuation based calculations I think are noisier). Else you need to check if the Boltzmann distributions are being correctly generated: See the code and paper describing it linked here: https://github.com/shirtsgroup/checkensemble On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Can I ask a question concerning your previous email, I followed Cv = (dU/dT)_V Cp = (dH/dT)_P for my lutidine molecule, and I get same values for Cv and Cp. But when I test with kB T^2 c_P = Var (Enthalpy) kB T^2 c_V = Var (Energy) I get 40 J/mol.K difference in Cv and Cp. Mean that fluctuation play big role. Which way of checking I can rely? Best regards On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com wrote: By definition (more fundamental that fluctuation formulas) Cv = (dU/dT)_V Cp = (dH/dT)_P Run two simulations at different T and estimate the derivatives. On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, I still would like to know what was your method you mentioned on last paragraph, just for learning: ''Also, to be sure, you should double check by calculating both heat capacities by finite difference formulas as well with two simulations at T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls don't agree within propagated error, then something is off.'' ? thanks Best regards On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Andre, thank you for the link, you are probably right, It seems that my molecule has the difference Cp-Cv in the same range as benzene (since it has also ring structure). Best regards On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, I use Parrinello-Rahman for barostat and v-rescale for thermostat. Sorry, could you explain more the second paragraph please? I did not get
Re: [gmx-users] GPU acceleration
On Wed, Jun 10, 2015 at 4:21 AM, Alex nedoma...@gmail.com wrote: At this point, we will be getting the card for sure, likely the GTX 960 you suggested. Hence, a question. Which of the manufacturers would you recommend in terms of cooling (if you think it might become an issue with week or so long runs)? I can't really give you much recommendation in terms of manufacturer. I typically suggest people to stay away from factory overclocked cards (although some have been reporting stable use for years of such cards). Otherwise the GTX 960 is not a beast in terms of power consumption and I would not expect cooling to be much of an issue. I doubt we'll be needing the 4GB version, so my only concern is cooling. Comments highly appreciated. Thanks, Alex -- 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] Different Cv and Cp
Dear Faezeh, Michael is absolutely right, both methods should yield exactly the same Cp and Cv values, but that is only true in the limit of infinite sampling. If sampling is not infinite but is long enough, Cp and Cv values should agree within the statistical uncertainty of each method. So it seems to me that you have improve your simulations until you get this agreement. regardless of which method you are using to compute Cp and Cv and based on your last messages, I think that you should try some more best practice testing before deciding whether Cv and Cp should be the same or not (that's your decision, not ours): (1) I would suggest you not to take the last frame of the NPT simulation as the correct volume. You should instead take an average volume from the equilibrated NPT simulation and then edit the gro file to reach that average volume. (2) are you sure that 10 ns is enough to properly sample heat capacities? Regarding this topic, I could ask you several questions: - Have you checked that all relevant structural and energetic patterns are fully relaxed within this time scale? For instance, energy components, density, radial distribution functions, relative orientation between molecules and so on. - Have you discarded the frames before structural and energetic relaxations were achieved? - Considering that lutidine is slightly bulky and has a well defined dipole moment, it may take a while for a full rotational relaxation. Have you computed the rotational correlation function to be sure that it relaxed long before 10 ns? If it did not relax, then 10 ns is not enough. - I like to compute these fluctuation-based properties as cumulative averages along the simulation (after structural and energetic relaxations, of course), it is easier to see if the average is approaching some plateau value (if not, longer simulation time is required). - I have never tested myself (has anyone tested?), but fluctuation-based calculations are obviously sensitive to the quality of the fluctuation, and double precision integration yields less noisier raw data than single precision integration does, so I would guess that double precision mdrun might provide a better-quality sampling of the fluctuation and would then improve the quality of your Cp and Cv estimates (just guessing). As I already stated (and provided you published experimental data in support of my statement), Cp and Cv need not be the same for molecular liquids. But it is up to you to prove that your simulations are reliable (my questions above are just a fraction of the checks you need to perform in order to convince yourself and your audience that you have obtained reliable data and not just simulation artifacts). In principle, you should include these checks in the supporting information of your manuscripts to convince the editors and referees (and the general audience after publication) that you have been thorough in your investigation. best Andre On Wed, Jun 10, 2015 at 9:54 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Could you please comment on my last question, thanks a lot. I have noticed that when I run both NVT and NPT simulations from a same .gro file (obtained from energy minimization) I obtain same Cv and Cp for two ensembles. However, so far I was running NVT after NPT (meaning I used .gro file obtained from NPT as initial configuration for NVT, since I wanted to have correct volume). The second way gives that big difference in Cv and Cp. I run a long simulations in all cases, but why both ways produce such difference? Best regards On Tue, Jun 9, 2015 at 5:45 PM, Michael Shirts mrshi...@gmail.com wrote: The variance formula is derived from the derivative formula + the assumption the distribution in Boltzmann, so they must agree if the distribution is Boltzmann. On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Thank you so much for the reply. Yes, I use contact applied pressure and I am careful about units. I checked and average enthalpy and U are close, meaning that PV is negligible. But the point is variance of enthalpy in NPT differs from variance of energy in NVT and that causes the difference. You had given me an article showing that for example for Benzene the difference in Cv and Cp is 25%, and here Ii get similar ( my molecule is also carbon ring). But still I can answer why two both ways does not give same Cv-Cp. I will follow your suggestion. Best regards On Tue, Jun 9, 2015 at 5:29 PM, Michael Shirts mrshi...@gmail.com wrote: If the simulation are generating configurations with the Boltzmann probability distribution, the results should the same up to error. Cv and Cp should not be exactly the same, though for liquids at room temperature, they are pretty close (look up the precise numbers for the fluid you are interested in). Are you calculating
Re: [gmx-users] Questions about the topology file format
If I am not mistaken, and there is a chance that I am the length and force constant are used with grompp in ffbonded.itp in the force field directory. After the question mark everything else is indeed not read so it is mostly used by the users for clarification. But I believe that in the part that you posted it is used in case you want to add some optional parameters you remove the mark. Hopefully I am right, but please if it is not much do double check my comments. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, June 3, 2015 8:58 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Questions about the topology file format On 6/3/15 1:55 PM, Ebert Maximilian wrote: Hi there, I have two quick questions about the topology file format which I couldn’t find in the documentary. The semi-colon is giving me some headache. Is it always a comment which is written after? First: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_135 1 IPAC11-0.111600 12.01100 ; qtot -0.112 CT is qtot and CT used for anything and is it interpreted since it is after the ; Everything after ; is ignored. Second: [ bonds ] ; ai aj funct r k 1 2 1 ;1.5350e-012.5363e+05 ; C1 - C2 CT - CT are the values for r and k here used since they are after the ; and what is C1-C2 and CT-CT used for and why another ;? Not used for anything. Whatever software you used to produce the topology annotated it for whatever reason that the programmer decided was useful and in whatever manner he/she liked. -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] creating index for first hydration layer water molecules
Thanks for the reply Justin. I have tried the following: g_select -f prodrun.xtc -s prodrun.tpr -n index.ndx -os size.xvg - oc cfrac.xvg -oi index.dat -select 'Nearby water resname SOL and within 0.35 of group Protein' But there is a syntax error. Could you please tell me where i could be going wrong.. On Tue, Jun 9, 2015 at 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/9/15 5:11 AM, Sahithya S Iyer wrote: Dear Users, The first hydration layer, to the best of my understanding, is the first minimum in the protein (backbone)-water radial distribution function. How do I create an index for the water molecules in the first hydration layer? The hydration layer around a protein includes the full protein, not just the backbone. You can, of course, analyze whatever makes sense to you, but the whole protein is typically considered in most experiments, and certainly is the case if anyone talks about the protein hydration layer. gmx select can do this. See examples in the help info. -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. -- Sahithya S Iyer -- 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] which file to use to analyze trajectory using code
Thanks Oliver ! On Tue, Jun 9, 2015 at 7:24 PM, Oliver Stueker ostue...@gmail.com wrote: Hello Sahithya, the xdrfile library is only one of many ways to write your own code trajectory analysis. Other options are: - Use share/gromacs/template/template.cpp ( template.c for Gromacs before 5.0) to write your own analysis tool in C++ (or C). - Use one of the following Python packages to write your analysis tool in Python: - pmx (formerly pymacs) https://code.google.com/p/pmx/ - MDAnalysis http://www.mdanalysis.org/ - MDTraj http://mdtraj.org/latest/ - I believe one can also write plugins for VMD (in tcl or python) Cheers, Oliver On Tue, Jun 9, 2015 at 3:33 AM, Sahithya S Iyer sah2...@gmail.com wrote: Thanks for the link Eric ! I am unable to open the following link though - ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz On Tue, Jun 9, 2015 at 9:31 AM, Eric Smoll ericsm...@gmail.com wrote: Hello Sahithya, Here is one solution: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library Best, Eric On Mon, Jun 8, 2015 at 9:56 PM, Sahithya S Iyer sah2...@gmail.com wrote: Dear users, If one wanted to analyze the trajectory obtained on production run for a property of the protein that is not already defined in the gromacs programs, which file should be used for analysis ? If one were to write an external code to analyze this property, .trr, .tpr, .xtc files cannot be used as they are binary files. How then can the trajectory be analyzed ? Thanks for your time -- 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. -- Sahithya S Iyer -- 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. -- Sahithya S Iyer -- 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] GPU acceleration
Well, I've had a Gigabyte-made OC'd GTX 660 at home (for gaming) for a few years, no problems at all. I guess my question was more along the lines of whether GPU MD runs are equivalent to week-long gaming in terms of heat production. What I also didn't know is whether 960 was a fiery beast. Your post answers that and we'll be getting one, probably from ASUS. I try to stay away from EVGA (terrible experience, card was returned, but I kept the Powered by EVGA sticker, which is now proudly presented on my toilet). Thanks. Alex SP I can't really give you much recommendation in terms of manufacturer. SP I typically suggest people to stay away from factory overclocked cards SP (although some have been reporting stable use for years of such SP cards). Otherwise the GTX 960 is not a beast in terms of power SP consumption and I would not expect cooling to be much of an issue. -- 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] Radius of gyration
Dear gromacs experts, I tried to analysis the Radius of gyration of a polymer. But I found the result of first frame was always very different. Then I installed different vesions of gmx with or without mpi. And I got different results. So I used the first tutorial on http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html as a example. I import the mases from the top file to matlab, and got the positions via vmd. It seems only 5.0.4 vesion without mpi get the correct result. While all the others have the same wrong number. But when I copy the file to another machine, I get another different false result. So where the problem come from? Thanks, Kangjie Lv 489524...@qq.com My result:(protein rg of frame 0) vesion 4.6.7 with mpi: 0 1.36815 1.16912 1.34953 0.74539 10 1.38857 1.17871 1.382170.745979 withoutmpi: 0 1.36815 1.16912 1.34953 0.74539 10 1.38857 1.17871 1.382170.745979 vesion 5.0.4 with mpi: 0 1.36815 1.16912 1.34953 0.74539 10 1.38857 1.17871 1.382170.745979 withoutmpi: 0 1.40022 1.19943 1.02439 1.19718 10 1.41136 1.20202 1.04328 1.2044 from matlab: 0 14.0022 10 14.1135 another machine(has 64 cores): vesion 5.0.4 with mpi (the first frame always false using different -b flags) 0 1.4657 1.38007 1.12533 1.06095 10 2.15321 1.45292 1.74791 2.02645 without mpi 0 1.40022 1.19943 1.02439 1.19718 10 1.41136 1.20202 1.04328 1.2044 all files here http://pan.baidu.com/s/1hq9yFsw -- 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] Ion binding to DNA
Hello, I am asked by one of the reviewers of my paper about the distribution of ions ( Mg2+) bound to a single stranded DNA as a function of simulation time at different salt concentrations. In order to do that I have calculated the RDF of ions from the closest atom of DNA using g_rdf with surf mol and res_com option at different time intervals. The first peak minima came around 5 angstrom and I calculated the number of ions in that cut-off at different time intervals with the -cn option of g_rdf. Then I am plotting it as no.of ions bound to DNA against time. what I want to ask is there anything wrong with this approach? I have referred to the work below http://www.tandfonline.com/doi/pdf/10.1080/07391102.2012.732344 Is there some other ways ( command or tool wise ) where the calculations are more accurate as far as the ion binding approach is concerned? Thanks for your time in advance Soumadwip Ghosh Research Scholar IITB india -- 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.
