Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote: Hi Justin, Yes, I am trying the course-grain model using gromacs, an absolute newer. My current model is not complex, just including 22 big atoms, only 4 base pair. What is the use of summing the entire base into one particle? The only coarse-grain FF I know anything about is MARTINI, which uses 4:1 mapping, i.e. 4 atoms represented by 1 particle. I would suspect that for 4 base pairs, one would have significantly more particles than 22 with this type of mapping scheme. You may be missing some of the subtleties of the base pair interactions by lumping a whole base into one particle. The total charges are zero . And I just include water atoms and DNA strands in my case. I guess maybe there is something wrong with their original positions. I am trying to modify the coordinate. Well, then you don't have DNA :) The backbone of DNA bears a negative charge at physiological pH, and thus contributes to the overall stability (and somewhat to the instability) of the helix. I would suggest refining your model a bit to reflect the physiological model. -Justin Thank you for your further suggestions. Yang From: Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 1:38 PM To: He, Yang; Gromacs Users' List Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi Justin, In my case, my box size is adequate to avoid interaction of periodic images of your DNA .For this point, I think is ok. In fact, when I run this simulation especially for the low temperature, one atom's(Tb1) behavior is strange .No matter how low the temperature is , it will separate from the other matching pair . The others are normal. It looks like you're working with some sort of coarse-grain model for DNA. If you're developing new parameters, welcome to the headaches that come with such derivations! Interaction between whatever Tb1 (thymine base?) and the other atoms may need to be modified. Are you summing the entire base into one particle? That's pretty extensive mapping that may not capture all the H-bonding interactions, but I guess that's up to you to decide. How about ions? Do you have a neutral solution, or do you have unsatisfied charges from the backbone? That may affect the dynamics as well. -Justin I list my nb and bon file in the attachments . Thank you From: Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 1:07 PM To: He, Yang; Gromacs Users' List Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi Justin, My box size is 3.13690 3.73000 2.7 and I use the user-defined potential functions. Is that box size adequate to avoid interaction of periodic images of your DNA? Typical B-DNA is about 2 nm wide, if 2.7 nm is the width of your box, I'd bet you're getting artefactual PBC interactions. #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 #include "ffyxhnb.itp" #include "ffyxhbon.itp" Well, if you're defining your own potential, I'd look there for spurious repulsive terms. If the DNA is shearing apart, your repulsion between atoms may be too large. Combine that with artefactual PBC interactions, and that may give rise to your strange behavior. This is my ffyxh.itp file Also I have change the value of tau_t by 0.1 but it did not work. Please let me know if you need any further information. The entirety of the .mdp file, and what you've defined in your *nb.itp *bon.itp files, in case there's anything obviously wrong. -Justin Thank you. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 12:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.001 ref_t= 300 I don't know if this is relevant or not, but a coupling constant of 0.001 is exceptionally short. What is the timestep in your simulation? Typically one sees tau_t = 0.1 with a timestep of 0.001-0.002 ps. ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility
Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote: Hi Justin, In my case, my box size is adequate to avoid interaction of periodic images of your DNA .For this point, I think is ok. In fact, when I run this simulation especially for the low temperature, one atom's(Tb1) behavior is strange .No matter how low the temperature is , it will separate from the other matching pair . The others are normal. It looks like you're working with some sort of coarse-grain model for DNA. If you're developing new parameters, welcome to the headaches that come with such derivations! Interaction between whatever Tb1 (thymine base?) and the other atoms may need to be modified. Are you summing the entire base into one particle? That's pretty extensive mapping that may not capture all the H-bonding interactions, but I guess that's up to you to decide. How about ions? Do you have a neutral solution, or do you have unsatisfied charges from the backbone? That may affect the dynamics as well. -Justin I list my nb and bon file in the attachments . Thank you From: Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 1:07 PM To: He, Yang; Gromacs Users' List Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi Justin, My box size is 3.13690 3.73000 2.7 and I use the user-defined potential functions. Is that box size adequate to avoid interaction of periodic images of your DNA? Typical B-DNA is about 2 nm wide, if 2.7 nm is the width of your box, I'd bet you're getting artefactual PBC interactions. #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 #include "ffyxhnb.itp" #include "ffyxhbon.itp" Well, if you're defining your own potential, I'd look there for spurious repulsive terms. If the DNA is shearing apart, your repulsion between atoms may be too large. Combine that with artefactual PBC interactions, and that may give rise to your strange behavior. This is my ffyxh.itp file Also I have change the value of tau_t by 0.1 but it did not work. Please let me know if you need any further information. The entirety of the .mdp file, and what you've defined in your *nb.itp *bon.itp files, in case there's anything obviously wrong. -Justin Thank you. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 12:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.001 ref_t= 300 I don't know if this is relevant or not, but a coupling constant of 0.001 is exceptionally short. What is the timestep in your simulation? Typically one sees tau_t = 0.1 with a timestep of 0.001-0.002 ps. ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 It will also disassociate .It is strange. So the dissociation occurs at 0K and 300K? Sounds like something is fundamentally flawed with your system setup. How large is your box? What force field are you using? -Justin Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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/s
RE: [gmx-users] the temperature effect in the simulation
Hi Yuguang, when I use the command ngmx to show the trajectory , I just choose the DNA group not including the water. Any suggestions ? Thank you very much. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mu Yuguang (Dr) [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 12:17 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the temperature effect in the simulation Do you have water ? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay Sent: 2008年11月12日 4:15 To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: > Hi all users, > > When I change the temperature to try to get different disassociation about > the two DNA's strands. But even I change the value of temperature by 0K in > the mdp file , > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = berendsen > ; Groups to couple separately > tc-grps = System > ; Time constant (ps) and reference temperature (K) > tau_t= 0.001 > The coupling constant sounds a bit small. The dynamics of fast motions may be affected more than you want, but I'm not a specialist of DNA and I don't know if it's a problem in that particular case. > ref_t= 300 > This indicates that your target temperature is 300K not 0K > ; Pressure coupling > Pcoupl = no > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p= 0.5 > compressibility = 4.5e-5 > ref_p= 1.0 > ; Random seed for Andersen thermostat > andersen_seed= 815131 > > It will also disassociate .It is strange. > > Can anyone of you tell me what is the reason for that? > > Thank you in advance. > > Yang > ___ > 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] the temperature effect in the simulation
He, Yang wrote: Hi Justin, My box size is 3.13690 3.73000 2.7 and I use the user-defined potential functions. Is that box size adequate to avoid interaction of periodic images of your DNA? Typical B-DNA is about 2 nm wide, if 2.7 nm is the width of your box, I'd bet you're getting artefactual PBC interactions. #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 #include "ffyxhnb.itp" #include "ffyxhbon.itp" Well, if you're defining your own potential, I'd look there for spurious repulsive terms. If the DNA is shearing apart, your repulsion between atoms may be too large. Combine that with artefactual PBC interactions, and that may give rise to your strange behavior. This is my ffyxh.itp file Also I have change the value of tau_t by 0.1 but it did not work. Please let me know if you need any further information. The entirety of the .mdp file, and what you've defined in your *nb.itp *bon.itp files, in case there's anything obviously wrong. -Justin Thank you. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 12:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.001 ref_t= 300 I don't know if this is relevant or not, but a coupling constant of 0.001 is exceptionally short. What is the timestep in your simulation? Typically one sees tau_t = 0.1 with a timestep of 0.001-0.002 ps. ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 It will also disassociate .It is strange. So the dissociation occurs at 0K and 300K? Sounds like something is fundamentally flawed with your system setup. How large is your box? What force field are you using? -Justin Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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 -- 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
RE: [gmx-users] the temperature effect in the simulation
Hi Justin, My box size is 3.13690 3.73000 2.7 and I use the user-defined potential functions. #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 #include "ffyxhnb.itp" #include "ffyxhbon.itp" This is my ffyxh.itp file Also I have change the value of tau_t by 0.1 but it did not work. Please let me know if you need any further information. Thank you. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 12:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: > Hi all users, > > When I change the temperature to try to get different disassociation about > the two DNA's strands. But even I change the value of temperature by 0K in > the mdp file , > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = berendsen > ; Groups to couple separately > tc-grps = System > ; Time constant (ps) and reference temperature (K) > tau_t= 0.001 > ref_t= 300 I don't know if this is relevant or not, but a coupling constant of 0.001 is exceptionally short. What is the timestep in your simulation? Typically one sees tau_t = 0.1 with a timestep of 0.001-0.002 ps. > ; Pressure coupling > Pcoupl = no > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p= 0.5 > compressibility = 4.5e-5 > ref_p= 1.0 > ; Random seed for Andersen thermostat > andersen_seed= 815131 > > It will also disassociate .It is strange. So the dissociation occurs at 0K and 300K? Sounds like something is fundamentally flawed with your system setup. How large is your box? What force field are you using? -Justin > > Can anyone of you tell me what is the reason for that? > > Thank you in advance. > > Yang > ___ > 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 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] the temperature effect in the simulation
Do you have water ? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay Sent: 2008年11月12日 4:15 To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: > Hi all users, > > When I change the temperature to try to get different disassociation about > the two DNA's strands. But even I change the value of temperature by 0K in > the mdp file , > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = berendsen > ; Groups to couple separately > tc-grps = System > ; Time constant (ps) and reference temperature (K) > tau_t= 0.001 > The coupling constant sounds a bit small. The dynamics of fast motions may be affected more than you want, but I'm not a specialist of DNA and I don't know if it's a problem in that particular case. > ref_t= 300 > This indicates that your target temperature is 300K not 0K > ; Pressure coupling > Pcoupl = no > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p= 0.5 > compressibility = 4.5e-5 > ref_p= 1.0 > ; Random seed for Andersen thermostat > andersen_seed= 815131 > > It will also disassociate .It is strange. > > Can anyone of you tell me what is the reason for that? > > Thank you in advance. > > Yang > ___ > 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] the temperature effect in the simulation
He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.001 The coupling constant sounds a bit small. The dynamics of fast motions may be affected more than you want, but I'm not a specialist of DNA and I don't know if it's a problem in that particular case. ref_t= 300 This indicates that your target temperature is 300K not 0K ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 It will also disassociate .It is strange. Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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 begin:vcard fn:Nicolas SAPAY n:SAPAY;Nicolas org:University of Calgary;Biological Sciences adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:PhD tel;work:(403) 220-6869 tel;fax:(403) 289-9311 x-mozilla-html:TRUE version:2.1 end:vcard ___ 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] the temperature effect in the simulation
He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.001 ref_t= 300 I don't know if this is relevant or not, but a coupling constant of 0.001 is exceptionally short. What is the timestep in your simulation? Typically one sees tau_t = 0.1 with a timestep of 0.001-0.002 ps. ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 It will also disassociate .It is strange. So the dissociation occurs at 0K and 300K? Sounds like something is fundamentally flawed with your system setup. How large is your box? What force field are you using? -Justin Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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
