[gmx-users] Eror: No parallel Ewald use PME instead!
Dear All users, I have encounter this error: - Fatal error: No parallel Ewald. Use PME instead. -- I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ewald method because my system can not converge using PME it heats up my system. Are there any suggestions? -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Confusion about itp file generated by topolbuild
Thanks for your reply Justin, but my confusion in the first part is not being removed. If #define is outdated then is it that gromacs does not even consider those lines? Then how does gromacs use those force fields during grompp? Also, if somehow gormacs considers those force fields then where is the location of them. There is no force field with such names in the working directory, neither in topolbuild directory nor in gromacs top directory . Regards On Tuesday, June 3, 2014 6:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/3/14, 6:51 AM, Bikramjit Sharma wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 #include ffbennb.itp #include ffusernb.itp What is the meaning of first 3 lines? Because there is no force field with any of these names (appeared in those lines) in the working directory and we are not assigning any path. So I am confused. Those #define statements are somewhat outdated; I don't think Gromacs uses them in any way. They used to be needed in old versions, but not any more. Also, following suggestions from gromacs user list (https://www.mail-archive.com/gmx-users@gromacs.org/msg12722.html), I have commented the last two lines of this itp file. So, the non bonded parameter file generated by topolbuild is not used. Is it correct? That depends on whether or not those files introduce any new parameters that your molecule needs. If they do, commenting them out isn't correct. If they only contain duplicate information already present in the parent force field, commenting them out is fine. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_membed itp file
Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr I face with this fatal error: Fatal error: Topology include file ffoplsaalipid.itp not found Now I want to know how can I create this itp file? Best wishes, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear All users, I have encounter this error: - Fatal error: No parallel Ewald. Use PME instead. -- I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ewald method because my system can not converge using PME it heats up my system. Are there any suggestions? -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_membed itp file
Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr I face with this fatal error: Fatal error: Topology include file ffoplsaalipid.itp not found Now I want to know how can I create this itp file? Best wishes, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Remove rotation around the center of mass
On Wed, Jun 4, 2014 at 1:01 AM, gmail wenjin.brooks...@gmail.com wrote:
Dear gmx-users,
I have some questions on the way that gromacs remove the rotation around
the center of mass when set comm-mode = Angular”
I have checked the related code for removing the rotation and have a
question on how gromacs estimate the inertia tensor I.
In gromacs, the inertia tensor is estimated as follows,
I=sum m_i*[x_i*x_i]-M*[x_c*x_c]
here, m_i is the mass of atom i;
x_i is the Cartesian coordinate of atom i;
x_c is the center of mass;
M is the total mass of the system.
[x*x] represents the outer product between x and x.
One can easily get that
I=sum m_i*[y_i*y_i] with y_i = x_i - x_c ———(1)
However, from standard mechanics textbook, the inertia is given as
I=sum m_i*{(y_i.y_i)E - [y_i*y_i]} (2)
here, y_i.y_i is the inner product between y_i and y_i;
E is a 3*3 identity matrix.
I want to know the reason that gromacs use Eq. (1) instead of Eq. (2) to
calculate the inertia tensor.
Without having looked at the code, I imagine GROMACS would calculate the
moment of inertia about the specified center, rather than bothering with
computing the tensor. Eq (2) is expressed in coordinates relative to an
arbitrary origin, to what does it reduce if you choose the COM as the
origin?
Mark
Since gromacs estimate the angular velocity (w) with
w=I^-1*L
Here, I^-1 is the inverse of the inertia tensor I;
L is the angular momentum.
The angular velocity will be different using Eq. (1) comparing to Eq. (2)
Does anyone know why gromacs use Eq. (1) not Eq. (2)?
Thanks,
Wenjin
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[gmx-users] No such moleculetype ZN
Dear Justin/ *Dhanachandra * *thanks for your reply* *as you konw, i simulated Zinc cation on hGH protein* *and received an error in energy minimization process in em.tpr production(*grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr)*, as below:* *No such moleculetype ZN* *in one hand, i checked my ions.itp file and saw there is no ZN ion in it, but atp file in my choosed force field (opls) support ZN ion same CU ion (about CU cation, i had not any problem)* *on the other hand, by genion command, i could replace ZN ions instead of sol (water) molecules, easily* *i don,t know it,s related to my version pf gromacs 4.6.5 or not?* *Regards* *elham tazikeh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in mdrun
I have been doing simulation of 216 SPC molecules with cubic box dimension 3 nm.I have set the cut off at 1.2 nm but I get this error during mdrun one of the box vectors has become shorter than twice the cut-off or box_yy-|box_zy| or box_zz has become smaller than the cut-off error The box vector is greater than double than twice the cut-off but I don't seem to understand the other possible errors.How can I resolve them? -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
Dear Mark, Thank you for your reply. When you do not change any parameters except one thing in mdp file(PME to ewald as the paper said that)and then your system converges, for me it means the problem is related to choosing the right method for calculation of the electrostatic potential energy. What's your point on it? - Mark wrote: Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmojarad at gmail.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users wrote: * Dear All users, ** I have encounter this error: ** - ** Fatal error: ** No parallel Ewald. Use PME instead. ** -- ** I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ** ewald method because ** my system can not converge using PME it heats up my system. Are there any ** suggestions? ** -- ** Sincerely ** Ali Alizadeh ** --* -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
I performed an NVT simulation. On Wed, Jun 4, 2014 at 3:12 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mark, Thank you for your reply. When you do not change any parameters except one thing in mdp file(PME to ewald as the paper said that)and then your system converges, for me it means the problem is related to choosing the right method for calculation of the electrostatic potential energy. What's your point on it? - Mark wrote: Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmojarad at gmail.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users wrote: * Dear All users, * * I have encounter this error: ** - ** Fatal error: ** No parallel Ewald. Use PME instead. ** -- ** I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ** ewald method because ** my system can not converge using PME it heats up my system. Are there any ** suggestions? ** -- ** Sincerely ** Ali Alizadeh * * --* -- Sincerely Ali Alizadeh -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in mdrun
Harshkumar, If you are using NPT ensamble, volume will not fix. After some time as box length decrease than cut-off, you will get such type of error. You can increase number of water molecules or decrease cut-off. On Wed, Jun 4, 2014 at 4:06 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I have been doing simulation of 216 SPC molecules with cubic box dimension 3 nm.I have set the cut off at 1.2 nm but I get this error during mdrun one of the box vectors has become shorter than twice the cut-off or box_yy-|box_zy| or box_zz has become smaller than the cut-off error The box vector is greater than double than twice the cut-off but I don't seem to understand the other possible errors.How can I resolve them? -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- PRAVEEN KUMAR Research scholar INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH PUNE -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in mdrun
Ok.Thanks! On Wed, Jun 4, 2014 at 6:47 AM, Praveen Kumar pravink...@gmail.com wrote: Harshkumar, If you are using NPT ensamble, volume will not fix. After some time as box length decrease than cut-off, you will get such type of error. You can increase number of water molecules or decrease cut-off. On Wed, Jun 4, 2014 at 4:06 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I have been doing simulation of 216 SPC molecules with cubic box dimension 3 nm.I have set the cut off at 1.2 nm but I get this error during mdrun one of the box vectors has become shorter than twice the cut-off or box_yy-|box_zy| or box_zz has become smaller than the cut-off error The box vector is greater than double than twice the cut-off but I don't seem to understand the other possible errors.How can I resolve them? -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- PRAVEEN KUMAR Research scholar INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH PUNE -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Non-bonded interactions
Dear justin, Shall I introduce this calculated non-bonded interaction values in gromos43a1.ff ( ffninbonded.itp) section or specifically I can include them in my protein topology file ? ([nonbond_param]) ? On 6/3/14, 4:56 AM, ? wrote: Dear Justin, I have calculated upon the way you provided as follows : CHARMM Rmin/2 - Gromacs sigma: multiply by 2 to get Rmin, convert to sigma by multiplying by 2^(-1/6), then multiply by 0.1 to convert A - nm Sigma = 3.83 Rmin = (3.83 * 2) 7.66 * 2^(-1/6)*0.1 = 0.682428418 Epsilon: multiply the CHARMM value by 4.184 to convert kcal/mol to kJ/mol Epsilon 0.0262 x 4.184 = 0.1096208 Is that right conversion?, if so, I have used g_sigeps utility in gromacs for above mentioned sigma and epsion values and got entirely different values: g_sigeps -sig 3.83 -eps 0.0262 c6 = 3.30791e+02, c12 = 1.04411e+06 sigma = 3.83000, epsilon = 0.02620 Van der Waals minimum at 4.29903, V = -0.0262 Fit of Lennard Jones (12-6) to Buckingham: A = 4264.18, B = 2.79133, C = 330.791 Please advice if i am making any mistake ? You're not supplying the right values to g_sigeps. It's designed to convert known values of sigma and epsilon (already in Gromacs units) to C6/C12, which is not what you need to accomplish. The value you're passing to -sig is actually Rmin, not sigma, and the value you're supplying to -eps is in the wrong units. The converted values you obtained with by-hand calculation (not g_sigeps) appear reasonable. Verifying the energy reported by CHARMM/NAMD and Gromacs should be a simple test to confirm. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
On Wed, Jun 4, 2014 at 12:42 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mark, Thank you for your reply. When you do not change any parameters except one thing in mdp file(PME to ewald as the paper said that)and then your system converges, for me it means the problem is related to choosing the right method for calculation of the electrostatic potential energy. What's your point on it? My point is that a flawed model physics, or a flawed system preparation, can get lucky and run stably, or not. On the information given, there is no reason to suppose that changing the kind of reciprocal-space approximation is relevant. Last time I heard a report like this, the person had changed various nonbonded settings to make things run faster, and in so doing produced a junk model physics. Mark - Mark wrote: Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmojarad at gmail.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users wrote: * Dear All users, * * I have encounter this error: ** - ** Fatal error: ** No parallel Ewald. Use PME instead. ** -- ** I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ** ewald method because ** my system can not converge using PME it heats up my system. Are there any ** suggestions? ** -- ** Sincerely ** Ali Alizadeh ** --* -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] No such moleculetype ZN
Hi, It's hard to understand what you're doing, but take care to distinguish atom name, residue name, and moleculetype name, which can all be different depending on the GROMACS version and force field. Mark On Wed, Jun 4, 2014 at 10:50 AM, elham tazikeh elham.tazi...@gmail.com wrote: Dear Justin/ *Dhanachandra * *thanks for your reply* *as you konw, i simulated Zinc cation on hGH protein* *and received an error in energy minimization process in em.tpr production(*grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr)*, as below:* *No such moleculetype ZN* *in one hand, i checked my ions.itp file and saw there is no ZN ion in it, but atp file in my choosed force field (opls) support ZN ion same CU ion (about CU cation, i had not any problem)* *on the other hand, by genion command, i could replace ZN ions instead of sol (water) molecules, easily* *i don,t know it,s related to my version pf gromacs 4.6.5 or not?* *Regards* *elham tazikeh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Non-bonded interactions
On 6/4/14, 7:27 AM, 라지브간디 wrote: Dear justin, Shall I introduce this calculated non-bonded interaction values in gromos43a1.ff ( ffninbonded.itp) section or specifically I can include them in my protein topology file ? ([nonbond_param]) ? Neither. I have said it twice before, and I'll say it a third time - the parameters you have cannot be sensibly combined with others in the Gromos96 43A1 parameter set. They were developed for CHARMM; they need to be used with a CHARMM force field. Hacking them into some other force field breaks the internal self-consistency of the force field and you end up with a junk simulation. The proper approach is to introduce the parameters in [atomtypes] of ffnonbonded.itp in the CHARMM force field and let the combination rules do the rest of the work. -Justin On 6/3/14, 4:56 AM, ? wrote: Dear Justin, I have calculated upon the way you provided as follows : CHARMM Rmin/2 - Gromacs sigma: multiply by 2 to get Rmin, convert to sigma by multiplying by 2^(-1/6), then multiply by 0.1 to convert A - nm Sigma = 3.83 Rmin = (3.83 * 2) 7.66 * 2^(-1/6)*0.1 = 0.682428418 Epsilon: multiply the CHARMM value by 4.184 to convert kcal/mol to kJ/mol Epsilon 0.0262 x 4.184 = 0.1096208 Is that right conversion?, if so, I have used g_sigeps utility in gromacs for above mentioned sigma and epsion values and got entirely different values: g_sigeps -sig 3.83 -eps 0.0262 c6 = 3.30791e+02, c12 = 1.04411e+06 sigma = 3.83000, epsilon = 0.02620 Van der Waals minimum at 4.29903, V = -0.0262 Fit of Lennard Jones (12-6) to Buckingham: A = 4264.18, B = 2.79133, C = 330.791 Please advice if i am making any mistake ? You're not supplying the right values to g_sigeps. It's designed to convert known values of sigma and epsilon (already in Gromacs units) to C6/C12, which is not what you need to accomplish. The value you're passing to -sig is actually Rmin, not sigma, and the value you're supplying to -eps is in the wrong units. The converted values you obtained with by-hand calculation (not g_sigeps) appear reasonable. Verifying the energy reported by CHARMM/NAMD and Gromacs should be a simple test to confirm. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in mdrun
On 6/4/14, 6:47 AM, Praveen Kumar wrote: Harshkumar, If you are using NPT ensamble, volume will not fix. After some time as box length decrease than cut-off, you will get such type of error. You can increase number of water molecules or decrease cut-off. Decreasing the cutoff may work to get rid of the error, but there can be consequences in the validity of the physics if you make ad hoc changes just to get the simulation to run, or run faster... -Justin On Wed, Jun 4, 2014 at 4:06 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I have been doing simulation of 216 SPC molecules with cubic box dimension 3 nm.I have set the cut off at 1.2 nm but I get this error during mdrun one of the box vectors has become shorter than twice the cut-off or box_yy-|box_zy| or box_zz has become smaller than the cut-off error The box vector is greater than double than twice the cut-off but I don't seem to understand the other possible errors.How can I resolve them? -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] No such moleculetype ZN
On 6/4/14, 4:50 AM, elham tazikeh wrote: Dear Justin/ *Dhanachandra * *thanks for your reply* *as you konw, i simulated Zinc cation on hGH protein* *and received an error in energy minimization process in em.tpr production(*grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr)*, as below:* *No such moleculetype ZN* *in one hand, i checked my ions.itp file and saw there is no ZN ion in it, but atp file in my choosed force field (opls) support ZN ion same CU ion (about CU cation, i had not any problem)* *on the other hand, by genion command, i could replace ZN ions instead of sol (water) molecules, easily* *i don,t know it,s related to my version pf gromacs 4.6.5 or not?* If the force field has parameters for ZN, then simply add the appropriate [moleculetype] to ions.itp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_membed itp file
On 6/4/14, 4:06 AM, h.aliza...@znu.ac.ir wrote: Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr I face with this fatal error: Fatal error: Topology include file ffoplsaalipid.itp not found Now I want to know how can I create this itp file? How did you generate the .top file that includes this .itp file? It looks like it relies on some modified version of the OPLS-AA force field, with added lipid parameters. That's not going to be standard in Gromacs, so it's likely dependent upon some external source. Given the naming convention of the file, it was probably designed for some old version of Gromacs, but can certainly be made to work if you actually obtain the necessary force field files. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Confusion about itp file generated by topolbuild
On 6/4/14, 2:25 AM, Bikramjit Sharma wrote: Thanks for your reply Justin, but my confusion in the first part is not being removed. If #define is outdated then is it that gromacs does not even consider those lines? Then how does gromacs use those force fields during grompp? As Mark pointed out, depending on which version of Gromacs you are using, grompp may need those directives to parse ions.itp or water topologies. In the 5.0 series, such #define statements are largely irrelevant. Also, if somehow gormacs considers those force fields then where is the location of them. There is no force field with such names in the working directory, neither in topolbuild directory nor in gromacs top directory . I have no idea what topolbuild expects or provides. It likely should have generated the nonstandard parameters and written them somewhere. -Justin Regards On Tuesday, June 3, 2014 6:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/3/14, 6:51 AM, Bikramjit Sharma wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 2 yes0.50.8333 #include ffbennb.itp #include ffusernb.itp What is the meaning of first 3 lines? Because there is no force field with any of these names (appeared in those lines) in the working directory and we are not assigning any path. So I am confused. Those #define statements are somewhat outdated; I don't think Gromacs uses them in any way. They used to be needed in old versions, but not any more. Also, following suggestions from gromacs user list (https://www.mail-archive.com/gmx-users@gromacs.org/msg12722.html), I have commented the last two lines of this itp file. So, the non bonded parameter file generated by topolbuild is not used. Is it correct? That depends on whether or not those files introduce any new parameters that your molecule needs. If they do, commenting them out isn't correct. If they only contain duplicate information already present in the parent force field, commenting them out is fine. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] No such moleculetype for ZN
On 6/4/14, 12:48 PM, elham tazikeh wrote: Dear Justin Thanks for your answer. Based on your answer, I will add following lines to ions.itp file in opls force field: [ moleculetype ]; molnamenrexcl ZN 1 [ atoms ]; idat typeres nr residu nameat name cg nrcharge mass 1Zn2+ 1ZN ZN 1 2 65.37000 Is my manner true?! Well, there's one way to find out... I don't have Zn parameters in my version of OPLS-AA; have you added them yourself? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
Dear Justin, here is my mdp file: title = Liquid CO2 NVT ; Run parameters integrator = md-vv nsteps = 200 dt = 0.001 emtol = 1.0 emstep = 0.0001 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 100 ; Bond parameters continuation = no constraint_algorithm = lincs constraints = all-bonds ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.25 rcoulomb = 1.25 rvdw = 1.25 ; Electrostatics coulombtype = ewald fourierspacing = 0.6 ; Temperature coupling is on tcoupl = nose-hoover tc-grps = system tau_t = 0.1 ref_t = 300 ; Pressure coupling is off pcoupl = no ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = -1 On 6/4/14, 8:29 AM, Ali Alizadeh wrote: Dear Mark, In my first simulation we had these lines: ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT --- ; Electrostatics coulombtype= ewald; Particle Mesh Ewald for long-range electrostatics fourierspacing= 0.6; grid spacing for FFT - My system in 2nd case is equilibrated. For anyone to make sense of what you're doing, you'll need to provide complete .mdp files (those settings are not the only determining factors of the validity of the model physics) and evidence of what you're deciding is equilibrated, stable, etc (i.e. real numbers and output from whatever relevant analysis). -Justin On Wed, Jun 4, 2014 at 4:35 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Jun 4, 2014 at 12:42 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mark, Thank you for your reply. When you do not change any parameters except one thing in mdp file(PME to ewald as the paper said that)and then your system converges, for me it means the problem is related to choosing the right method for calculation of the electrostatic potential energy. What's your point on it? My point is that a flawed model physics, or a flawed system preparation, can get lucky and run stably, or not. On the information given, there is no reason to suppose that changing the kind of reciprocal-space approximation is relevant. Last time I heard a report like this, the person had changed various nonbonded settings to make things run faster, and in so doing produced a junk model physics. Mark - Mark wrote: Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmojarad at gmail.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users wrote: * Dear All users, * * I have encounter this error: ** - ** Fatal error: ** No parallel Ewald. Use PME instead. ** -- ** I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ** ewald method because ** my system can not converge using PME it heats up my system. Are there any ** suggestions? ** -- ** Sincerely ** Ali Alizadeh ** --* -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] No such moleculetype ZN
Dear Justin Please ignore my previous questions. I want to do 2 md simulations: 1) protein and Cu, 2) protein and Zn. After checking force fields in gromacs 4.5.3, I found oplsaa in which there are both Cu and Zn ions in atomtype.atp file. Then I used gromacs 4.6.5 (with opls force field) to do md simulations. I added ions to my system using genion command. genion -s ions.tpr -o sol_ions.gro -p topol.top -pname CU -pq +2 -neutral -conc 0.025. genion -s ions.tpr -o sol_ions.gro -p topol.top -pname ZN -pq +2 -neutral -conc 0.025. In both cases, ions were added without problem. Then, I used grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr In case of protein and Cu, there is not problem. But, in case of protein and Zn, I encountered error: No such moleculetype ZN. I checked ions.itp in opls force field in gromacs 4.6.5, I found, there are both Cu and Zn ions in atomtype.atp file. But, there is only Cu in ions.itp file. How to do md simulation of protein-zn system using gromacs 4.6.5. Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Intra molecular force correction for SPME
On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
Thanks for providing a small fraction of the information for which Justin asked. You stand a much better chance of ever getting an answer from volunteers if you provide more detail than you think could ever be relevant. :-) Mark On Wed, Jun 4, 2014 at 7:39 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Justin, here is my mdp file: title = Liquid CO2 NVT ; Run parameters integrator = md-vv nsteps = 200 dt = 0.001 emtol = 1.0 emstep = 0.0001 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 100 ; Bond parameters continuation = no constraint_algorithm = lincs constraints = all-bonds ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.25 rcoulomb = 1.25 rvdw = 1.25 ; Electrostatics coulombtype = ewald fourierspacing = 0.6 ; Temperature coupling is on tcoupl = nose-hoover tc-grps = system tau_t = 0.1 ref_t = 300 ; Pressure coupling is off pcoupl = no ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = -1 On 6/4/14, 8:29 AM, Ali Alizadeh wrote: Dear Mark, In my first simulation we had these lines: ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT --- ; Electrostatics coulombtype= ewald; Particle Mesh Ewald for long-range electrostatics fourierspacing= 0.6; grid spacing for FFT - My system in 2nd case is equilibrated. For anyone to make sense of what you're doing, you'll need to provide complete .mdp files (those settings are not the only determining factors of the validity of the model physics) and evidence of what you're deciding is equilibrated, stable, etc (i.e. real numbers and output from whatever relevant analysis). -Justin On Wed, Jun 4, 2014 at 4:35 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Jun 4, 2014 at 12:42 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mark, Thank you for your reply. When you do not change any parameters except one thing in mdp file(PME to ewald as the paper said that)and then your system converges, for me it means the problem is related to choosing the right method for calculation of the electrostatic potential energy. What's your point on it? My point is that a flawed model physics, or a flawed system preparation, can get lucky and run stably, or not. On the information given, there is no reason to suppose that changing the kind of reciprocal-space approximation is relevant. Last time I heard a report like this, the person had changed various nonbonded settings to make things run faster, and in so doing produced a junk model physics. Mark - Mark wrote: Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmojarad at gmail.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users wrote: * Dear All users, * * I have encounter this error: ** - ** Fatal error: ** No parallel Ewald. Use PME instead. ** -- ** I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use ** ewald method because ** my system can not converge using PME it heats up my system. Are there any ** suggestions? ** -- ** Sincerely ** Ali Alizadeh ** --* -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Intra molecular force correction for SPME
Dear Mark, For the paper please refer http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf;. While calculating the forces in SPC/E water, H-O, H-H forces in the same molecule will be calculated in reciprocal space due to the property of Particle Mesh technique. Do you mean to say that this will be compensated by SHAKE/SETTLE? Won't it affect the net force acting on the molecule if we don't remove it? Sumith YD Date: Wed, 4 Jun 2014 21:26:31 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Cc: Discussion list for GROMACS users gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s=tr5ex0jdn3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help gm1
hi... I'm starting in Gromacs and gm1 I'm working with, I have formed micelles with gm1, but I could not make the topology file, I've tried with martini but I get an error grompp. would greatly appreciate your help, thank you very much Lic Biochemistry Leonardo Villalba Ministerio de Ciencia y Tecnologia Cordoba Cordoba, Argentina -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Out of disk space
Choosing appropriate output-frequency settings, nsteps to cap your file
size, and mdrun -noappend is likely your best approach.
Mark
On Wed, Jun 4, 2014 at 8:54 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia carlosfami...@gmail.com
wrote:
Hello,
I was running the final equilibration step (NTP) and i received an error
saying that i was running out of disk space, the trajectory file writen
has
2GB, and every retry will generate a file with the same size. I have
looked
for file size limit, but there is no limitation that i can find on my
system. I am runing arch linux on a 32bits computer (i686),
That is likely a limitation that is manifest in whatever library stack is
supporting the file writing that GROMACS is using. If (say) the C library
uses a 32-bit integer for the size, bang you're dead.
the file system
is ext4, have 2GB of ram, and 64GB of disk available.
The command issued was:
mdrun -v -deffnm npt
The gromacs message was:
Program mdrun, VERSION 4.6.5
Source code file:
.../aur-gromacs-mpi/src/gromacs-4.6.5/src/gmxlib/trnio.c, line: 311
File input/output error:
Cannot write trajectory frame; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the
GROMACS
I have also runned the comman ulimit -a, that showed:
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 30
file size (blocks, -f) unlimited
pending signals (-i) 16117
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size(512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 99
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 16117
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
Additionally i run a program to write 2.5 GB to disk in c++, that
generated
the 2.5GB file without any problem:
#include iostream
#include fstream
#include vector
int main()
{
std::vectorchar empty(1024, 0);
std::ofstream ofs(ouput.img, std::ios::binary | std::ios::out);
for(int i = 0; i 1024*2560; i++)
{
if (!ofs.write(empty[0], empty.size()))
{
std::cerr problem writing to file std::endl;
return 255;
}
}
}
Any ideas on how to solve this?
Use a 64-bit operating system ;-) This is a problem users of your
operating system have likely encountered before, so if there is (say) a C
library that is compiled in some kind of 64-bit work-around mode, you may
be able to use that. The C++ library seems like it may have such a back end.
I know that i can change the parameters in the mdp file in order to
generate smaller files, but i was looking for a different solution that
wouldn't require this.
Is there any option to mdrun that could split the trajectory file for a
specified size?
No.
Mark
Thanks,
Carlos Família
--
Carlos Familia, MSc , PharmD
ISCSEM Pharmacology Assistant Lecturer
ISCSEM Laboratory of Molecular Pathology Researcher
Tel. +351 212946700 (Main) / +351 212946769 (Lab)
e-mail: carlosfami...@gmail.com / carlosfami...@egasmoniz.edu.pt
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Re: [gmx-users] No such moleculetype ZN
On 6/4/14, 2:25 PM, elham tazikeh wrote: Dear Justin Please ignore my previous questions. I want to do 2 md simulations: 1) protein and Cu, 2) protein and Zn. After checking force fields in gromacs 4.5.3, I found oplsaa in which there are both Cu and Zn ions in atomtype.atp file. Then I used gromacs 4.6.5 (with opls force field) to do md simulations. I added ions to my system using genion command. genion -s ions.tpr -o sol_ions.gro -p topol.top -pname CU -pq +2 -neutral -conc 0.025. genion -s ions.tpr -o sol_ions.gro -p topol.top -pname ZN -pq +2 -neutral -conc 0.025. In both cases, ions were added without problem. Then, I used grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr In case of protein and Cu, there is not problem. But, in case of protein and Zn, I encountered error: No such moleculetype ZN. I checked ions.itp in opls force field in gromacs 4.6.5, I found, there are both Cu and Zn ions in atomtype.atp file. But, there is only Cu in ions.itp file. How to do md simulation of protein-zn system using gromacs 4.6.5. It may not be possible, but that's a force field issue, not a software issue. Most force fields don't cover more than a few metal ions, and even then the parameters for transition metals are generally incapable of capturing the true physical behavior of these ions. Such is the limitation of additive MM force fields. The Zn parameters were indeed removed from OPLS; their parameters were either undocumented or found to be incorrect. So it is possible to use 4.5.3 to make things work, but the parameters you're applying are not trustworthy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help gm1
On 6/4/14, 5:00 PM, leonardo villalba wrote: hi... I'm starting in Gromacs and gm1 I'm working with, I have formed micelles with gm1, but I could not make the topology file, I've tried with martini but I get an error grompp. would greatly appreciate your help, thank you very much What exactly do you need help with? If you need help, you need to be specific. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
