[gmx-users] about specbond
Dear all, I'm trying to run a simulation of a ligand bound to an enzyme.I make a specbond between ligand and residue, Is this bond proper for EM or MD simulation? What parameters are defined on it? Thank you 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] about specbond
Rui Li wrote: Dear all, I'm trying to run a simulation of a ligand bound to an enzyme.I make a specbond between ligand and residue, Is this bond proper for EM or MD simulation? What parameters are defined on it? if grompp doesn't complain there are parameters for angles and bonds etc. Use gmxdump to find out which values. Thank you 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Error in topology file
Dear Experts, Hi ! I am doing simulation of cholera toxin, one with GTP( guanosine triphosphate) and other without it.The without GTP MD simulation I have done, now I started the other and when I used the pdb2gmx command on pdb file it says: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue 'GTP' not found in residue topology database Earlier this already happen so I left that and was started the pdb having GTP removed but this time it is necessary for me.Should I use prodrg server or some thing else. Hoping for guidance. Lal badshah. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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] Error in topology file
This will be helpful for you: http://wiki.gromacs.org/index.php/Exotic_Species and other information from gromacs wiki. Andreas From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of s lal badshah Sent: 16 April 2008 11:12 To: gromacs Subject: [gmx-users] Error in topology file Dear Experts, Hi ! I am doing simulation of cholera toxin, one with GTP( guanosine triphosphate) and other without it.The without GTP MD simulation I have done, now I started the other and when I used the pdb2gmx command on pdb file it says: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue 'GTP' not found in residue topology database Earlier this already happen so I left that and was started the pdb having GTP removed but this time it is necessary for me.Should I use prodrg server or some thing else. Hoping for guidance. Lal badshah. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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] VdW and Coulomb SR contribution to dVdl in thermodynamic integration
Oh dear, yes I do use a soft core potential and I overlooked that I set sc-power to 1. So even at lamda=0 there should be a soft core contribution to dV/dl! Thanks Berk. I guess you are using soft-core interactions. In that case there are more terms in dV/dl, see eq. 4.120 in the manual. Berk. Date: Mon, 14 Apr 2008 18:13:32 +0200 From: reich at mpikg.mpg.de To: gmx-users at gromacs.org Subject: [gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration Dear Gromacs-users, I have been doing a test thermodynamic integration for the conversion of methanol into a dummy molecule in water. I have been interested in the contribution of the VdW and Coulomb short range interaction to dVdl. According to equations 4.108 and 4.104, at lambda=0 (the methanol-state) the contributions should be the negative Lennard-Jones and Coulomb short range interaction energies between methanol and the surrounding water. I have been calculating the interaction energies with g_energy (choosing LJ-SR:methanol-rest and Coul-SR:methanol-rest as options). For example for a particular step in my trajectory I get -7.954321 kJ/mol for the Lennard-Jones interaction and -56.966656 kJ/mol for the Coulomb intercation between methanol and water. So the contribution of the combined interactions to dVdl should be 64.921 kJ/mol I have, however, also used the option sepdvdl with mdrun to get some detailed information on dVdl during the simulation. The line from the log-file giving me the contribution of Lennard-Jones and Coulomb short range interactions for the simulation step in question is: VdW and Coulomb SR particle-p. V -1.49467e+04 dVdl 1.01145e+03 So the simulation output gives me a result that is two magnitudes greater than what I calculated! Is there anything wrong with my reasoning or do you have any other clue why I end up with two different results? Thanks Luther ___ 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 make choices of COM in the system with freeze group?
Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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 constraint structure not conformation
Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was thinking in use some position restrain in the backbone atoms of the domains and leave the linkers and all the side chains to move freely but this aproach will not let the system to change the conformation. I'm using GROMACS 3.2.1. With a dihedral constraint it will be posible to what I want to do? How can I do it? There is any other option to do this? Best Regards, Anthony ___ 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] how to make choices of COM in the system with freeze group?
I'm not sure that I interpret your question correctly, but my guess is that you want to remove the center-of-mass translation and/or rotation. You can set this in the .mdp file with the commands comm_mode and comm_grps and an appropriate index file. Please refer to the manual or the online mdp option reference for the details: http://www.gromacs.org/documentation/reference/online/mdp_opt.html - Daniel On Apr 16, 2008, at 16:26, tuyusong wrote: Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of- mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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 --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone) +46-18-511 755 (fax) http://xray.bmc.uu.se/~larsson [EMAIL PROTECTED] ___ 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] how to make choices of COM in the system with freeze group?
You can opt for 3). If your system only compose of nanotube and water, why freeze it? Regards, Yang Ye tuyusong wrote: Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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
[gmx-users] Conformation Search with Gromacs
Dear USERS, Can one use Gromacs for conformation search? If yes, how? Thanks, Adama _ Adama Tandia Modeling Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ 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] structure files of water and CNT
Hello, I am a new user of Gromacs and want to simulate water transport through Carbon nanotubes. Where can I find structure files of water and CNT? Thank you so much! Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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] Conformation Search with Gromacs
Tandia, Adama wrote: Dear USERS, Can one use Gromacs for conformation search? If yes, how? If you mean systematic search the answer is no. You can do energy minimization or MD. Thanks, Adama _ Adama Tandia Modeling Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] structure files of water and CNT
Quoting Hero [EMAIL PROTECTED]: Hello, I am a new user of Gromacs and want to simulate water transport through Carbon nanotubes. Where can I find structure files of water and CNT? I believe there is an online server for generating CNT structures; check the list archives thoroughly and you will find it. Water is in $GMXLIB/top. -Justin Thank you so much! Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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 [EMAIL PROTECTED] | (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] Warning message with 3.3.3 but not with 3.3.1
Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. ___ 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] Warning message with 3.3.3 but not with 3.3.1
Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Warning message with 3.3.3 but not with 3.3.1
Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Warning message with 3.3.3 but not with 3.3.1
tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Warning message with 3.3.3 but not with 3.3.1
David wrote: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Thank you for replying. Do you mean, that it must be nothing when system has any freeze groups? Yusong. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 4:01 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Warning message with 3.3.3 but not with 3.3.1
tuyusong wrote: David wrote: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Thank you for replying. Do you mean, that it must be nothing when system has any freeze groups? Yusong. yes. that should work. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 4:01 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] structure files of water and CNT
quote who=Hero Hello, I am a new user of Gromacs and want to simulate water transport through Carbon nanotubes. Where can I find structure files of water and CNT? Last summer I put a walk though with the basics for this. It can be found at: http://cs86.com/CNSE/SWNT.htm Although please note that this was not put together for the most current version so some of the files my have changed... So consult the most current version of the GROMACS manual. Hope this helps! ~Chris Thank you so much! Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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 Christopher Dale Stiles Cell: 315-247-8620 ___ 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] Warning message with 3.3.3 but not with 3.3.1
Thanks David. So to speak, as the center of mass of group SOL is not free to move, we do not need stopcm to it. Another question is, does it would be problematic in long time simulation without stopcm in such situation, I mean the systematic errors caused by center of mass motion. Thanks for clarification. tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 48, Issue 48 *** ___ 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] about nmr refinement
dear users, I want to do a NMR refinement of a protein structure that comes from CYANA, (torsion angle dynamics), to include the interacctions betwen protein with the solvent, and improve the quality of the structure, my question is about the protocol that i should do, i have read the manual but i dont know if i need to do annealing simulation, or position restricted dynamics or use nmr refinement and how i should choose the parameters, is there any manual to do that? thanks in advance ROGELIO HERNANDEZ - ¡Capacidad ilimitada de almacenamiento en tu correo! No te preocupes más por el espacio de tu cuenta con Correo Yahoo!: http://correo.yahoo.com.mx/___ 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] how to make choices of COM in the system with freeze group?
You can opt for 3). If your system only compose of nanotube and water, why freeze it? Thank Yang Ye, we are doing some tests on effects of T-coupling caused by removing COM in the system with freeze groups Regards, Yusong tuyusong wrote: Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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 ___ 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] Warning message with 3.3.3 but not with 3.3.1
Bo wrote: Thanks David. So to speak, as the center of mass of group SOL is not free to move, we do not need stopcm to it. Another question is, does it would be problematic in long time simulation without stopcm in such situation, I mean the systematic errors caused by center of mass motion. Thanks for clarification. For a system with freeze group, we should not use any removal of com motions, and this system should still work. I don't find this relevant descriptions in gmx-manual, and it may be added into it. Yusong tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 48, Issue 48 *** ___ 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
