Re: [gmx-users] Model of water
I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
I used TIPS3P in everything, because after all, it's CHARMM's water and no reviewer can complain about using it with CHARMM. If you want a faster simulation you can try using the regular TIP3P and see if the bilayer metrics remain satisfactory for you. If you still have doubts, run simulations with both TIPS3P and TIP3P and decide if the differences are significant. IIRC Thomas Piggot's latest CHARMM36 Gromacs paper Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study has some results on POPC in TIP3P vs. TIPS3P. When using genbox, you always use spc216.gro as the starting solvent coordinates. The waters will adopt the correct physical properties specified by the model and forcefield during equilibration. On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote: As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
Thanks for your explanation. Do you mean genbox will adapt the model and the force field automatically? Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 3:27 PM Subject: Re: [gmx-users] Model of water I used TIPS3P in everything, because after all, it's CHARMM's water and no reviewer can complain about using it with CHARMM. If you want a faster simulation you can try using the regular TIP3P and see if the bilayer metrics remain satisfactory for you. If you still have doubts, run simulations with both TIPS3P and TIP3P and decide if the differences are significant. IIRC Thomas Piggot's latest CHARMM36 Gromacs paper Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study has some results on POPC in TIP3P vs. TIPS3P. When using genbox, you always use spc216.gro as the starting solvent coordinates. The waters will adopt the correct physical properties specified by the model and forcefield during equilibration. On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote: As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes. Then I ran genbox : #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top genbox added SOL but there is not any water model including in my top file, so I added #include charmm36.ff/tip3p.itp to top file manually: Next, I ran energy minimization. Is my procedure correct? How would I be sure that tip3p is used as water model? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 3:27 PM Subject: Re: [gmx-users] Model of water I used TIPS3P in everything, because after all, it's CHARMM's water and no reviewer can complain about using it with CHARMM. If you want a faster simulation you can try using the regular TIP3P and see if the bilayer metrics remain satisfactory for you. If you still have doubts, run simulations with both TIPS3P and TIP3P and decide if the differences are significant. IIRC Thomas Piggot's latest CHARMM36 Gromacs paper Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study has some results on POPC in TIP3P vs. TIPS3P. When using genbox, you always use spc216.gro as the starting solvent coordinates. The waters will adopt the correct physical properties specified by the model and forcefield during equilibration. On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote: As I studied in Beyond modeling by Peter Lai and coworkers, TIPS3P is the CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals interactions. So I guess I can use tips3p model of water instead of tip3p and go on. Correct? Then I need to know which model of water should be used in later simulations ( protein insertion in POPC) ? Is tips3p recommended? I'd like to know more about tips3p model. Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:54 AM Subject: Re: [gmx-users] Model of water I tried to use genbox, but there is not tip3p.gro in GROMACS package, so spc216.gro is recommended to be used. I want to know what exactly I need to do to get the popc in water with tip3p model of water? Thanks in advance. Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 11:28 AM Subject: [gmx-users] Model of water Dears, I got a link sent me by Peter Lai to simulate POPC in water: http://uab.hyperfine.info/~pcl/files/popc36/ He used TIP3SP, as it is apparent in its top file. I want to use simulate my own system of POPC in water with tip3p model of water? Is it possible to use its Peter's top and itp files? Please help me Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
On 10/6/12 8:59 AM, Shima Arasteh wrote: To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes. Then I ran genbox : #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top genbox added SOL but there is not any water model including in my top file, so I added #include charmm36.ff/tip3p.itp to top file manually: Next, I ran energy minimization. Is my procedure correct? How would I be sure that tip3p is used as water model? Your approach is correct. genbox will not write topology information (i.e. #include statements) to your topology for you. It adds coordinates to your configuration and updates the [molecules] section, nothing more. It is up to you to tell grompp what parameters to apply to the water molecules. If your topology #includes a TIP3P topology, that's what grompp will use. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 4:44 PM Subject: Re: [gmx-users] Model of water On 10/6/12 8:59 AM, Shima Arasteh wrote: To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes. Then I ran genbox : #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top genbox added SOL but there is not any water model including in my top file, so I added #include charmm36.ff/tip3p.itp to top file manually: Next, I ran energy minimization. Is my procedure correct? How would I be sure that tip3p is used as water model? Your approach is correct. genbox will not write topology information (i.e. #include statements) to your topology for you. It adds coordinates to your configuration and updates the [molecules] section, nothing more. It is up to you to tell grompp what parameters to apply to the water molecules. If your topology #includes a TIP3P topology, that's what grompp will use. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
Yes, the system is only POPC and water. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fwd: Re: [gmx-users] Model of water
Original Message Subject: Re: [gmx-users] Model of water Date: Sat, 06 Oct 2012 10:47:18 -0400 From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound#mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
# grep -c P popc-solv.gro 1628 What should I do with this number? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
On 10/6/12 10:52 AM, Shima Arasteh wrote: # grep -c P popc-solv.gro 1628 What should I do with this number? The letter P can theoretically match a lot of lines in a POPC system. Be sure you're grepping for a specific atom name, rather than something that can match both atom and residue names. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
The total atom of popc-solv.gro is 74672 grep HW gives me 48698 grep P gives me 1628 Section of moleculetypes in top file is as [ molecules ] Compound #mols POPC 238 SOL 24348 I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!! Please help me :( Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 6:22 PM Subject: Re: [gmx-users] Model of water # grep -c P popc-solv.gro 1628 What should I do with this number? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound #mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
On 10/6/12 11:52 AM, Shima Arasteh wrote: The total atom of popc-solv.gro is 74672 grep HW gives me 48698 Assuming you meant to type 48696 like you reported before, this means there are 24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If you grep for OW (since it is unique to each water molecule), you can confirm the count. grep P gives me 1628 I already said this grep was insufficiently precise and thus it is not possible to connect this information with the topology. Section of moleculetypes in top file is as [ molecules ] Compound#mols POPC 238 SOL 24348 I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!! You need to make the topology agree with the coordinate file. Do not make manual adjustments to the .gro file. Sometimes it's better to start over and be more careful. A mismatch between coordinates and topology always boils down to errors in bookkeeping. -Justin Please help me :( Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, October 6, 2012 6:22 PM Subject: Re: [gmx-users] Model of water # grep -c P popc-solv.gro 1628 What should I do with this number? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: Yes, the system is only POPC and water. Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: OK. I did as follow as I described, but there is an error: 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top Then added #include charmm36.ff/tip3p.itp to topol.top 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr Fatal error: number of coordinates in coordinate file (popc-solv.gro, 74672) does not match topology (topol.top, 104936) I checked the water molecules of popc-solv.gro by grep command ; # grep -c HW popc-solv.gro 48696 [ molecules ] ; Compound#mols POPC 238 SOL 24348 What is the problem? would you please help me? I think the SOL molecule are counted twice!! You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Model of water
Dear Justin, I downloaded popc.pdb file from http://terpconnect.umd.edu/~jbklauda/research/download.html. This pdb file has water molecules. So I tried to run these commands and don't run genbox: 1.editconf -f popc.pdb -o popc.gro -c -d 1.0 -bt cubic 2.grompp -f em.mdp -c popc.gro -p topol.top -o em.tpr I also added the SOL molecules manually as it is written at the end of the popc.pdb file downloaded. But this fatal errors comes out: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 2 in topol.top and popc.gro does not match (C12 - C11) Warning: atom name 3 in topol.top and popc.gro does not match (C13 - C12) Warning: atom name 4 in topol.top and popc.gro does not match (C14 - C13) Warning: atom name 5 in topol.top and popc.gro does not match (C15 - C14) Warning: atom name 6 in topol.top and popc.gro does not match (H12A - H11) Warning: atom name 7 in topol.top and popc.gro does not match (H12B - H12) Warning: atom name 8 in topol.top and popc.gro does not match (H13A - H21) Warning: atom name 9 in topol.top and popc.gro does not match (H13B - H22) Warning: atom name 10 in topol.top and popc.gro does not match (H13C - H23) Warning: atom name 11 in topol.top and popc.gro does not match (H14A - H31) Warning: atom name 12 in topol.top and popc.gro does not match (H14B - H32) Warning: atom name 13 in topol.top and popc.gro does not match (H14C - H33) Warning: atom name 14 in topol.top and popc.gro does not match (H15A - H41) Warning: atom name 15 in topol.top and popc.gro does not match (H15B - H42) Warning: atom name 16 in topol.top and popc.gro does not match (H15C - H43) Warning: atom name 17 in topol.top and popc.gro does not match (C11 - C15) Warning: atom name 18 in topol.top and popc.gro does not match (H11A - H51) Warning: atom name 19 in topol.top and popc.gro does not match (H11B - H52) Warning: atom name 20 in topol.top and popc.gro does not match (P - P1) Warning: atom name 21 in topol.top and popc.gro does not match (O13 - O3) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 36]: 8382 non-matching atom names atom names from topol.top will be used atom names from popc.gro will be ignored Analysing residue names: There are: 72 Other residues There are: 2242 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42393.00 Largest charge group radii for Van der Waals: 0.040, 0.040 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 96x96x96, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.59 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 191 Mb of data There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1584 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Would you please give me advice? Thanks for all your explanation. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 7:25 PM Subject: Re: [gmx-users] Model of water On 10/6/12 11:52 AM, Shima Arasteh wrote: The total atom of popc-solv.gro is 74672 grep HW gives me 48698 Assuming you meant to type 48696 like you reported before, this means there are 24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If you grep for OW (since it is unique to each water molecule), you can confirm the count. grep P gives me 1628 I already said this grep was insufficiently precise and thus it is not possible to connect this information with the topology. Section of moleculetypes in top file is as [ molecules ] Compound #mols POPC 238 SOL 24348 I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!! You need to make the topology agree with the coordinate file. Do not make manual adjustments to the .gro file. Sometimes it's better to start over and be more careful. A mismatch between coordinates and topology always boils down to errors
Re: [gmx-users] Model of water
On 10/6/12 1:27 PM, Shima Arasteh wrote: Dear Justin, I downloaded popc.pdb file from http://terpconnect.umd.edu/~jbklauda/research/download.html. This pdb file has water molecules. So I tried to run these commands and don't run genbox: 1.editconf -f popc.pdb -o popc.gro -c -d 1.0 -bt cubic If you have a pre-equilibrated membrane, complete with water, this doesn't make sense. You're introducing empty space around the whole system. 2.grompp -f em.mdp -c popc.gro -p topol.top -o em.tpr I also added the SOL molecules manually as it is written at the end of the popc.pdb file downloaded. I don't understand why you need to do this. But this fatal errors comes out: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 2 in topol.top and popc.gro does not match (C12 - C11) Warning: atom name 3 in topol.top and popc.gro does not match (C13 - C12) Warning: atom name 4 in topol.top and popc.gro does not match (C14 - C13) Warning: atom name 5 in topol.top and popc.gro does not match (C15 - C14) Warning: atom name 6 in topol.top and popc.gro does not match (H12A - H11) Warning: atom name 7 in topol.top and popc.gro does not match (H12B - H12) Warning: atom name 8 in topol.top and popc.gro does not match (H13A - H21) Warning: atom name 9 in topol.top and popc.gro does not match (H13B - H22) Warning: atom name 10 in topol.top and popc.gro does not match (H13C - H23) Warning: atom name 11 in topol.top and popc.gro does not match (H14A - H31) Warning: atom name 12 in topol.top and popc.gro does not match (H14B - H32) Warning: atom name 13 in topol.top and popc.gro does not match (H14C - H33) Warning: atom name 14 in topol.top and popc.gro does not match (H15A - H41) Warning: atom name 15 in topol.top and popc.gro does not match (H15B - H42) Warning: atom name 16 in topol.top and popc.gro does not match (H15C - H43) Warning: atom name 17 in topol.top and popc.gro does not match (C11 - C15) Warning: atom name 18 in topol.top and popc.gro does not match (H11A - H51) Warning: atom name 19 in topol.top and popc.gro does not match (H11B - H52) Warning: atom name 20 in topol.top and popc.gro does not match (P - P1) Warning: atom name 21 in topol.top and popc.gro does not match (O13 - O3) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 36]: 8382 non-matching atom names atom names from topol.top will be used atom names from popc.gro will be ignored These warnings suggest that the coordinate file is out of sync with respect to the atoms in the topology. Bad things will happen, because the wrong parameters are mapped to the wrong atoms. -Justin Analysing residue names: There are:72 Other residues There are: 2242 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42393.00 Largest charge group radii for Van der Waals: 0.040, 0.040 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 96x96x96, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.59 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 191 Mb of data There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1584 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Would you please give me advice? Thanks for all your explanation. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, October 6, 2012 7:25 PM Subject: Re: [gmx-users] Model of water On 10/6/12 11:52 AM, Shima Arasteh wrote: The total atom of popc-solv.gro is 74672 grep HW gives me 48698 Assuming you meant to type 48696 like you reported before, this means there are 24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If you grep for OW (since it is unique to each water molecule), you can confirm the count. grep P gives me 1628 I already said this grep was insufficiently precise and thus it is not possible to connect this information with the topology. Section of moleculetypes in top file is as [ molecules ] Compound#mols POPC 238
