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] 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
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
