[gmx-users] Dissipative Particle Dynamics (DPD)
Dear all, since one of my mails with multiple questions went completely unanswered ( http://www.mail-archive.com/gmx-users@gromacs.org/msg15437.html ), let me try this time with more specific question. Is there any chance of Dissipative Particle Dynamics (DPD) being incorporated in Gromacs as a companion (or even replacement) of Brownian Dynamics? According to the book Understanding Molecular Simulation by Frenkel and Smit (Second edition, 2002, page 467), Brownian Dynamics does not conserve momentum, does not obey Newton's 3rd law and hence does not recover correct hydrodynamic (Navier-Stokes) behaviour at large length and time scales, while DPD takes care of all these problems. In that case, wouldn't it be more appropriate to use this technique as a replacement of Brownian/Langevin dynamics? Regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate scaling factors in the LIE equation
Dear all, I hope van der waals and electrostatic scaling factors in the LIE equation (g_lie) are system dependent (Ref: DK Jones-hertzog et al. 1996). Any one please give me a suggestion to calculate Clj and Cqq (as per g_lie program) in my protein-ligand system. I used GROMOS96 43a2 force field (improved alkane dihedrals) with SPCE water molecules. Thank you very much in advance. Sincerely, Burri ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] QMMM
deAR --- On Mon, 1/9/08, Pradip Biswas [EMAIL PROTECTED] wrote: From: Pradip Biswas [EMAIL PROTECTED] Subject: Re: [gmx-users] QMMM To: [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 1 September, 2008, 3:04 AM I believe it supports GAMESS UK, not US. Gerrit ([EMAIL PROTECTED]) can assist you further. pb On Mon, Aug 25, 2008 at 4:30 AM, ha salem [EMAIL PROTECTED] wrote: hello I want install gromacs with gamess US for QMMM can you guide me for installation procedure thank you ___ gmx-users mailing list [EMAIL PROTECTED] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] QMMM
dear sir i am not aware of wheather interface is gamess UK or gamess US .but one thing if run configure -help command in terminal, it shows the option --with Gamess .sorry i am not able to reply correctely since i am beginner also in application side please sir be in touch .i am ver glad of your atonce reply thank you sir --- On Mon, 1/9/08, Pradip Biswas [EMAIL PROTECTED] wrote: From: Pradip Biswas [EMAIL PROTECTED] Subject: Re: [gmx-users] QMMM To: [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 1 September, 2008, 3:04 AM I believe it supports GAMESS UK, not US. Gerrit ([EMAIL PROTECTED]) can assist you further. pb On Mon, Aug 25, 2008 at 4:30 AM, ha salem [EMAIL PROTECTED] wrote: hello I want install gromacs with gamess US for QMMM can you guide me for installation procedure thank you ___ gmx-users mailing list [EMAIL PROTECTED] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Understanding of POPC analysis
Hi all, this may be trivial question to you. I am unfamiliar with gromacs. My doubt is that in POPC analysis most of the cases concerning about Z-axis why not X and Y. Can you please clear me this doubt. Thanks in advance for your suggestion. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Changing LJ potential
Dear All, I need to define the LJ potential in a new way. Could anybody tell me where the LJ potential is calculated in the GROMACS files. -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Understanding of POPC analysis
minnale wrote: Hi all, this may be trivial question to you. I am unfamiliar with gromacs. My doubt is that in POPC analysis most of the cases concerning about Z-axis why not X and Y. Can you please clear me this doubt. Thanks in advance for your suggestion. By convention, we think of bilayers in the x-y plane, with the normal to the bilayer lying along the z-axis. In a practical sense, it is also very convenient to use semiisotropic pressure coupling (applied in the x/y and z dimensions) for membranes. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Using .pdb only
Hi There, I am usinng gromacs for running MDS of one protein, Can I use the pdb file only without generating the .gro file i.e. without using pdb2gmx ? If no, then how can I avoid addition of hydrogen during pdb2gmx ? With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using .pdb only
vivek sharma wrote: Hi There, I am usinng gromacs for running MDS of one protein, Can I use the pdb file only without generating the .gro file i.e. without using pdb2gmx ? Theoretically, yes. Gromacs can read a number of file formats at any stage (.pdb, .gro, etc). If no, then how can I avoid addition of hydrogen during pdb2gmx ? Then you will probably have a broken (and useless) topology. Addition of hydrogens is dependent upon the force field you want to use. All atomistic force fields distributed with Gromacs require at least the inclusion of polar hydrogens. -Justin With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Bonds missing in VMD visualization
Hello, I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it all worked nicely. But when I try to visualize the trajectory file in VMD some of the C-Cl bonds are missing (although all the atoms appear on the screen - only bonds are missing)? Can I do anything to fix this? /Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Bonds missing in VMD visualization
VMD computes distances between pairs of atoms to draw a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb you open before the .xtc/.trr), this distance is greater than 2.0A. On Mon, Sep 1, 2008 at 10:45 AM, Andreas Kring [EMAIL PROTECTED] wrote: Hello, I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it all worked nicely. But when I try to visualize the trajectory file in VMD some of the C-Cl bonds are missing (although all the atoms appear on the screen - only bonds are missing)? Can I do anything to fix this? /Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_velacc
Dear Vitaly Chaban, Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. g_velacc: g_velacc -f -s -o -aceflen Since, mine is a single protein, I have not defined any index file and I am calculating the g_velacc on backbone atoms. as the manual says, -aceflen will define the number of frames to be taken into consideration i suppose. Here, though with the option -s we are calculting the momentum auto correlation function, but still we are considering it as velocity auto correlation funciton. Is it alright or as the other user mentioned we need to devide the correlation value with square of the mass of the protein ? g_analyze: here, the numerical integration is done by trapezium rule. Ideally we need to carryout the integration from 0 to infinity but since our auto correlation function is calculated on a short period of time (which is close to t=0), the integration is evaluated only on this period i suppose. The output I got is the following: Calculating the integral using the trapezium rule Integral 1 0.99279 +/-0.0 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 3.975160e-02 1.960813e-01 4.002493e-02 2.9396.669 is the 0.99279 is the integral value or any thing else ? Which value I can compare with the value obtained by g_msd. My g_msd value is 1.7*10^-6 cm**2/s which is reasonably good compared to the experimental value. Thanks and Regards, Ram. On Sun, Aug 31, 2008 at 2:18 PM, rams rams [EMAIL PROTECTED] wrote: How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. I still dont have any idea how to get the diffusion constant using g_velacc. Ram. On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban [EMAIL PROTECTED]wrote: No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. But it is not applicable in the anisotropic systems, for example in ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re[2]: [gmx-users] Re: g_velacc
Hi Ram, You should divide the value of your integral to the square of mass of you protein. Be attentive with units and powers then. I guess the final value will be essentially less than 0.99279 for floating protein. rr Here, though with the option -s we are calculting the momentum auto correlation function It seems to me you calculate the momentum ACF in all the cases using g_velacc. Maybe Florian could correct me if I'm wrong here. :) Vitaly rr Dear Vitaly Chaban, rr rr Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. rr rr g_velacc: rr rr g_velacc -f -s -o -aceflen rr rr Since, mine is a single protein, I have not defined any index file and I am calculating the g_velacc on backbone atoms. rr rr as the manual says, -aceflen will define the number of frames to be taken into consideration i suppose. rr rr Here, though with the option -s we are calculting the momentum auto correlation function, but still we are considering it as velocity auto correlation funciton. Is it alright or as the other user mentioned we need to devide the correlation value with square of the mass of the protein ? rr rr g_analyze: rr rr here, the numerical integration is done by trapezium rule. Ideally we need to carryout the integration from 0 to infinity but since our auto correlation function is calculated on a short period of time (which is close to t=0), the integration is evaluated only on this period i suppose. The output I got is the following: rr rr rr Calculating the integral using the trapezium rule rr Integral 1 0.99279 +/- 0.0 rrstd. dev. relative deviation of rrstandard- cumulants from those of rr set averagedeviation sqrt(n-1) a Gaussian distribition rrcum. 3 cum. 4 rr SS1 3.975160e-02 1.960813e-01 4.002493e-022.939 6.669 rr rr rr is the 0.99279 is the integral value or any thing else ? rr Yes, this is an integral value. But for diffusion constant divide it by M*M. rr Which value I can compare with the value obtained by g_msd. My g_msd value is 1.7*10^-6 cm**2/s which is reasonably good compared to the experimental value. rr rr rr Thanks and Regards, rr Ram. rr rr rr On Sun, Aug 31, 2008 at 2:18 PM, rams rams [EMAIL PROTECTED] wrote: rr rr How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. rr rr I still dont have any idea how to get the diffusion constant using g_velacc. rr rr Ram. rr rr rr rr On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban [EMAIL PROTECTED] wrote: rr No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. rr rr But it is not applicable in the anisotropic systems, for example in rr ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email:[EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_velacc
Hi Ram, You should divide the value of your integral to the square of mass of you protein. Be attentive with units and powers then. I guess the final value will be essentially less than 0.99279 for floating protein. rr Here, though with the option -s we are calculting the momentum auto correlation function It seems to me you calculate the momentum ACF in all the cases using g_velacc. Maybe Florian could correct me if I'm wrong here. :) Vitaly rr Dear Vitaly Chaban, rr rr Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. rr rr g_velacc: rr rr g_velacc -f -s -o -aceflen rr rr Since, mine is a single protein, I have not defined any index file and I am calculating the g_velacc on backbone atoms. rr rr as the manual says, -aceflen will define the number of frames to be taken into consideration i suppose. rr rr Here, though with the option -s we are calculting the momentum auto correlation function, but still we are considering it as velocity auto correlation funciton. Is it alright or as the other user mentioned we need to devide the correlation value with square of the mass of the protein ? rr rr g_analyze: rr rr here, the numerical integration is done by trapezium rule. Ideally we need to carryout the integration from 0 to infinity but since our auto correlation function is calculated on a short period of time (which is close to t=0), the integration is evaluated only on this period i suppose. The output I got is the following: rr rr rr Calculating the integral using the trapezium rule rr Integral 1 0.99279 +/-0.0 rr std. dev.relative deviation of rrstandard - cumulants from those of rr set average deviation sqrt(n-1) a Gaussian distribition rr cum. 3 cum. 4 rr SS1 3.975160e-02 1.960813e-01 4.002493e-02 2.9396.669 rr rr rr is the 0.99279 is the integral value or any thing else ? rr Yes, this is an integral value. But for diffusion constant divide it by M*M. rr Which value I can compare with the value obtained by g_msd. My g_msd value is 1.7*10^-6 cm**2/s which is reasonably good compared to the experimental value. rr rr rr Thanks and Regards, rr Ram. rr rr rr On Sun, Aug 31, 2008 at 2:18 PM, rams rams [EMAIL PROTECTED] wrote: rr rr How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. rr rr I still dont have any idea how to get the diffusion constant using g_velacc. rr rr Ram. rr rr rr rr On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban [EMAIL PROTECTED] wrote: rr No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. rr rr But it is not applicable in the anisotropic systems, for example in rr ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_velacc
Hi Vitaly Chaban, The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ? Ram. On Mon, Sep 1, 2008 at 11:54 AM, rams rams [EMAIL PROTECTED] wrote: Dear Vitaly Chaban, Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. g_velacc: g_velacc -f -s -o -aceflen Since, mine is a single protein, I have not defined any index file and I am calculating the g_velacc on backbone atoms. as the manual says, -aceflen will define the number of frames to be taken into consideration i suppose. Here, though with the option -s we are calculting the momentum auto correlation function, but still we are considering it as velocity auto correlation funciton. Is it alright or as the other user mentioned we need to devide the correlation value with square of the mass of the protein ? g_analyze: here, the numerical integration is done by trapezium rule. Ideally we need to carryout the integration from 0 to infinity but since our auto correlation function is calculated on a short period of time (which is close to t=0), the integration is evaluated only on this period i suppose. The output I got is the following: Calculating the integral using the trapezium rule Integral 1 0.99279 +/-0.0 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 3.975160e-02 1.960813e-01 4.002493e-02 2.9396.669 is the 0.99279 is the integral value or any thing else ? Which value I can compare with the value obtained by g_msd. My g_msd value is 1.7*10^-6 cm**2/s which is reasonably good compared to the experimental value. Thanks and Regards, Ram. On Sun, Aug 31, 2008 at 2:18 PM, rams rams [EMAIL PROTECTED] wrote: How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. I still dont have any idea how to get the diffusion constant using g_velacc. Ram. On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban [EMAIL PROTECTED]wrote: No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. But it is not applicable in the anisotropic systems, for example in ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_velacc
rams rams wrote: Hi Vitaly Chaban, The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ? yes. integration adds time in the denominator. Ram. On Mon, Sep 1, 2008 at 11:54 AM, rams rams [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear Vitaly Chaban, Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. g_velacc: g_velacc -f -s -o -aceflen Since, mine is a single protein, I have not defined any index file and I am calculating the g_velacc on backbone atoms. as the manual says, -aceflen will define the number of frames to be taken into consideration i suppose. Here, though with the option -s we are calculting the momentum auto correlation function, but still we are considering it as velocity auto correlation funciton. Is it alright or as the other user mentioned we need to devide the correlation value with square of the mass of the protein ? g_analyze: here, the numerical integration is done by trapezium rule. Ideally we need to carryout the integration from 0 to infinity but since our auto correlation function is calculated on a short period of time (which is close to t=0), the integration is evaluated only on this period i suppose. The output I got is the following: Calculating the integral using the trapezium rule Integral 1 0.99279 +/-0.0 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 3.975160e-02 1.960813e-01 4.002493e-02 2.9396.669 is the 0.99279 is the integral value or any thing else ? Which value I can compare with the value obtained by g_msd. My g_msd value is 1.7*10^-6 cm**2/s which is reasonably good compared to the experimental value. Thanks and Regards, Ram. On Sun, Aug 31, 2008 at 2:18 PM, rams rams [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. I still dont have any idea how to get the diffusion constant using g_velacc. Ram. On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. But it is not applicable in the anisotropic systems, for example in ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell
Fwd: Re[2]: [gmx-users] Re: g_velacc
rr Hi Vitaly Chaban, rr rr The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ? rr rr Ram. I've no time for exact recalculation now. My notes tell that the resulting integral value should be divided by M(mol)*M(mol)*1.66*1.66*10e-3. 1.66 and 10e-3 is from transformation from amu to kg. No 1/3 is needed. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban---BeginMessage--- rr Hi Vitaly Chaban, rr rr The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ? rr rr Ram. I've no time for exact recalculation now. My notes tell that the resulting integral value should be divided by M(mol)*M(mol)*1.66*1.66*10e-3. 1.66 and 10e-3 is from transformation from amu to kg. No 1/3 is needed. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email:[EMAIL PROTECTED] skype: vvchaban ---End Message--- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_velacc
Hi David Van der Spoel, You are right I missed the dt factor in the integral. Thanks a lot. Ram. On Mon, Sep 1, 2008 at 2:52 PM, David van der Spoel [EMAIL PROTECTED]wrote: rams rams wrote: Hi Vitaly Chaban, The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ? yes. integration adds time in the denominator. Ram. On Mon, Sep 1, 2008 at 11:54 AM, rams rams [EMAIL PROTECTED] mailto: [EMAIL PROTECTED] wrote: Dear Vitaly Chaban, Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. g_velacc: g_velacc -f -s -o -aceflen Since, mine is a single protein, I have not defined any index file and I am calculating the g_velacc on backbone atoms. as the manual says, -aceflen will define the number of frames to be taken into consideration i suppose. Here, though with the option -s we are calculting the momentum auto correlation function, but still we are considering it as velocity auto correlation funciton. Is it alright or as the other user mentioned we need to devide the correlation value with square of the mass of the protein ? g_analyze: here, the numerical integration is done by trapezium rule. Ideally we need to carryout the integration from 0 to infinity but since our auto correlation function is calculated on a short period of time (which is close to t=0), the integration is evaluated only on this period i suppose. The output I got is the following: Calculating the integral using the trapezium rule Integral 1 0.99279 +/-0.0 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 3.975160e-02 1.960813e-01 4.002493e-02 2.9396.669 is the 0.99279 is the integral value or any thing else ? Which value I can compare with the value obtained by g_msd. My g_msd value is 1.7*10^-6 cm**2/s which is reasonably good compared to the experimental value. Thanks and Regards, Ram. On Sun, Aug 31, 2008 at 2:18 PM, rams rams [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. I still dont have any idea how to get the diffusion constant using g_velacc. Ram. On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: No special reason, just mundane ones: computing the diffusion constant through mean square displacement is easier in terms of convergence. But it is not applicable in the anisotropic systems, for example in ones with spatial confinements present... :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] reg:merging of files
Dear users, I have a general question regarding the merging of files: 1. If suppose I am rerunning a job, the new tpr file is created in the following way: tpbconv -s .tpr1 -f .trr1 -o .tpr2 Here, no confusion. The run with new tpr2 would give me .trr2 file. Now if I want to rerun again, tpbconv -s tpr2 -f trr2 -o tpr3. In case, if I merge trr1 and trr2 to trr_total, and want to use the merged file to rerun, which tpr I shoud use for creating a new tpr file ? Precisely, tpbconv -s -f trr_total -o tpr3 Also, for analysis, do we need to merge all the tpr files or only the starting tpr file is enough ? What information exactly the tpr file holds ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] reg:merging of files
rams rams wrote: Dear users, I have a general question regarding the merging of files: 1. If suppose I am rerunning a job, the new tpr file is created in the following way: tpbconv -s .tpr1 -f .trr1 -o .tpr2 Here, no confusion. The run with new tpr2 would give me .trr2 file. Now if I want to rerun again, tpbconv -s tpr2 -f trr2 -o tpr3. In case, if I merge trr1 and trr2 to trr_total, and want to use the merged file to rerun, which tpr I shoud use for creating a new tpr file ? Precisely, tpbconv -s -f trr_total -o tpr3 Either one really. The important bits of information from the .tpr file are the parameters from the topology (bonded and nonbonded), all the different molecule definitions, and the .mdp parameters, which are generally constant during production runs. Coordinates and velocities are read from the .trr file. Don't forget to include the .edr file to get an exact continuation if you are applying temperature and/or pressure coupling! Also, for analysis, do we need to merge all the tpr files or only the starting tpr file is enough ? What information exactly the tpr file holds ? You cannot merge .tpr files. Do a gmxdump on your .tpr and you will see that there are no time-dependent quantities to stitch together. -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Bonds break while Minimising using distance restraints
Dear colleagues,
I need to use simple distance restraints of 12.5 A between two CA atoms of two
residues. I am using the following lines in the .itp file
#ifdef DDISRES
[distance_restraints]
;ai aj type index type' low up1 up2 fac
1703 1712 1 0 1 11.5 12.0 12.5 1.0
The first feww line of .mdp file for minimisation of protein alone is
; Preprocessing
;
title = ${MOL}
cpp = /lib/cpp ;Preprocessor
define = -DDISRES ;For cg, and also steep
After minimisation, the restarined residues the adjacent bonds
break. This results in fragmnets - residues alone, peptide bond alone and the
rest of the protein. The distance restrained residues seems to try to move
towards each other (6.04 A after minimisation) and this might have caused
fragmentation. I tried to use various upper and lower values for bond length so
as to increase flexibility. But, still I end up in the fragments.
Some of the suggestions in the archive says VMD doesn't show bonds if
they r above threshold value. When I checked the distances between the atoms,
one of them is really long CO-CA bond 3.23 A (normally its 1.59A). This means
the bond is no longer there.
I appreciate any suggestions in this regard.
Thanks regards,
Latha.
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Re: [gmx-users] Bonds break while Minimising using distance restraints
[EMAIL PROTECTED] wrote:
Dear colleagues,
I need to use simple distance restraints of 12.5 A between two CA atoms
of two residues. I am using the following lines in the .itp file
#ifdef DDISRES
[distance_restraints]
;ai aj type index type' low up1 up2 fac
1703 1712 10 111.5 12.0 12.5 1.0
The first feww line of .mdp file for minimisation of protein alone is
; Preprocessing
;
title = ${MOL}
cpp = /lib/cpp;Preprocessor
define = -DDISRES ;For cg, and also steep
You are not actually applying your distance restraint. If you have #ifdef
DDISRES, then you would have to define = -DDDISRES in the .mdp file. What
you probably meant to define was #ifdef DISRES in the topology.
After minimisation, the restarined residues the adjacent
bonds break. This results in fragmnets - residues alone, peptide bond
alone and the rest of the protein. The distance restrained residues
seems to try to move towards each other (6.04 A after minimisation) and
this might have caused fragmentation. I tried to use various upper and
lower values for bond length so as to increase flexibility. But, still I
end up in the fragments.
Bonds don't break in classical MD, this is just an artifact of visualization,
probably from nasty steric clashes within your structure.
Some of the suggestions in the archive says VMD doesn't show
bonds if they r above threshold value. When I checked the distances
between the atoms, one of them is really long CO-CA bond 3.23 A
(normally its 1.59A). This means the bond is no longer there.
No, the bond is there, VMD just isn't smart enough to see it :) You are
probably well on your way to an explosion if you try to constrain bond lengths
with LINCS, however.
-Justin
I appreciate any suggestions in this regard.
Thanks regards,
Latha.
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--
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Re: [gmx-users] Dissipative Particle Dynamics (DPD)
there is dpdmacs available.. Regards, Yang Ye - Original Message From: Suman Chakrabarty [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 1, 2008 5:50:15 PM Subject: [gmx-users] Dissipative Particle Dynamics (DPD) Dear all, since one of my mails with multiple questions went completely unanswered ( http://www.mail-archive.com/gmx-users@gromacs.org/msg15437.html ), let me try this time with more specific question. Is there any chance of Dissipative Particle Dynamics (DPD) being incorporated in Gromacs as a companion (or even replacement) of Brownian Dynamics? According to the book Understanding Molecular Simulation by Frenkel and Smit (Second edition, 2002, page 467), Brownian Dynamics does not conserve momentum, does not obey Newton's 3rd law and hence does not recover correct hydrodynamic (Navier-Stokes) behaviour at large length and time scales, while DPD takes care of all these problems. In that case, wouldn't it be more appropriate to use this technique as a replacement of Brownian/Langevin dynamics? Regards, Suman Chakrabarty.___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Strange behavior from steepest descents
Hi all, I'm preparing a few membrane protein systems using the InflateGRO script from Tieleman's site. The bilayer consists of 340 POPE lipids, using structures and topologies from the same site. I've prepared several systems (with other lipids) using the methodology described, but am running into some very strange behavior with the POPE system. I scaled the coordinates for the lipids by a factor of 4 and attempted a steepest descents minimization, my usual procedure. This step is essentially an in vacuo minimization of scaled lipids in the presence of a protein. The potential energy decreases nicely, and levels off. Suddenly, the potential plummets again, after which mdrun cuts out, reporting that it has converged to machine precision (although it has not reached my desired Fmax 1000). The forces were incredibly large (greater than 10^11), so there is definitely a problem with the system that I have yet to figure out. What troubles me is that mdrun believes the steepest descents algorithm has converged, when clearly it has not. I have posted an image here to illustrate the potential energy: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Images/Gromacs/weird_energy.jpg Conjugate gradients does not give the same result, instead converging to a potential energy of roughly -4 x 10^5, a reasonable magnitude, given the size of the system. The forces, however, remain large (10^5 or so), indicating I probably still have some clashes to resolve. Still I am troubled by the steepest descents result. Is this indicative of some problem? I usually use steepest descents, and have never had a problem with it before. I see the same result in serial or parallel (on 2 CPU's of my dual core laptop), using single-precision GMX 3.3.3. Thanks for reading yet another long email from me. The .mdp file I used for steepest descents (that gives the weird behavior) is below. The behavior persists even if I lower emtol and emstep, it just takes a bit longer to arrive at the same conclusion :) -Justin ===em.mdp ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Run control cpp = /usr/bin/cpp ; Preprocessor define = -DSTRONG_PR include = -I../ ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep emtol = 1000.0; Stop minimization when Fmax 1000 emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of steps energygrps = system; Which energy group(s) to write to disk ; Neighbor searching and electrostatics nstlist = 1 ns_type = simple rlist = 1.0 coulombtype = cut-off rcoulomb= 1.0 rvdw= 1.0 pbc = xyz === -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] COM monitoring
Dear users, Is it possible to monitor the center of mass motion of a protein using gromacs tools since this is the one to monitor in most of the dynamical studies of the protein. Thanks in advance. Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Differences in version 3.0 and 3.3
Hi Chris, Thanks for your reply. I pretty much only changed the executable. The top/itp files did have to be modified a little bit because the formats were different, but all the parameters were the same. I basically wrote a script to convert the formats. Besides all the other energy values were consistent except for the Coul-14 interactions. Daniel IHPC has moved to Fusionopolis with effect from 21st July 2008. There is no change to our email or telephone numbers. Our new address is : Institute of High Performance Computing, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632 This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate scaling factors in the LIE equation
Dear all, I hope van der waals and electrostatic scaling factors in the LIE equation (g_lie) are system dependent (Ref: DK Jones-hertzog et al. 1996). Any one please give me a suggestion to calculate Clj and Cqq (as per g_lie program) in my protein-ligand system. I used GROMOS96 43a2 force field (improved alkane dihedrals) with SPCE water molecules. Thank you very much in advance. Sincerely, Burri ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Potential energy of POPC
Hi all, I have done popc simulation for 5ns and calculated potential energy of POPC. The values started from -269000 kj/mol reduced to -272000 kj/mol. Could you please tell me 1.is it require to extend my simulation from 5ns? 2. The above mentioned potential energy values whether correct or not? Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dissipative Particle Dynamics (DPD)
Yang Ye wrote: there is dpdmacs available.. Yes, I know. But that seems to support only harmonic potential for even non-bonded interaction (DPD manual page 4-5), which is rather unphysical and not suitable for my purpose. Regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
